ENH: Support TD data by larsoner · Pull Request #11064 · mne-tools/mne-python

larsoner · 2022-08-21T19:50:09Z

@rob-luke how about this plan:

For now I'm inclined to make it so if you get a SNIRF_PROCESSED data type that we don't know how to handle, we should maybe raise an error in this case...? For now I've removed it as a coil_type because this _PROCESSED really seems to mean something else specific, and we should perhaps add those one by one as we find use cases for them.

I have some collaborators who have seen Kernel help files telling them to use this very out of date branch, so it would be nice to get this in!

…a type as outlined in the SNIRF specification document

…s, moments and processed (hbo/hbr)

rob-luke · 2022-08-23T11:04:27Z

Thanks for jumping in to finish this off @larsoner

For now I'm inclined to make it so if you get a SNIRF_PROCESSED data type that we don't know how to handle, we should maybe raise an error in this case...?

Agreed

Ping me when you want a review, it doesn't need to be a final review, I am happy to take a look early if that helps.

larsoner · 2022-08-23T11:26:53Z

Feel free to look now @rob-luke to see if you're happy with the overall design, the rest of the work is "just" some remaining details (adding unit tests, playing with the data a little bit to set scale factors, etc.) that I think we can rely on CIs to check, or that we can iterate on in follow-ups (e.g., tweaking plot scale factors)

rob-luke

Looking good, it will be great to have support for TD in MNE! I will review again once there are tests.

* upstream/main: (264 commits) BUG: Fix deprecated API usage in example (mne-tools#11512) Deprecate 'kind' and 'path' in favor of 'fname' in the layout reader (mne-tools#11500) EGI/MFF events outside EEG recording should not break the code (mne-tools#11505) fixed annotations error on export (mne-tools#11435) DOC: Update installer links [skip azp] [skip actions] [skip cirrus] (mne-tools#11506) BUG: updates for MPL 3.7 compatibility (mne-tools#11409) Fix docstrings by replacing str with path-like and fix double backticks for formatting (mne-tools#11499) Use pathlib.Path instead of os.path to handle files and folders [circle deploy] (mne-tools#11473) MAINT: Fix Circle [circle deploy] (mne-tools#11497) MAINT: Use mamba in CIs (mne-tools#11471) Updating documentation to clarify full vs half-bandwidth and defaults in time_frequency.multitaper.py (mne-tools#11479) Fix typo in tutorial (mne-tools#11498) Typo fix and added colons before code (mne-tools#11496) [MRG] ENH/DOC: demo custom spectrum creation (mne-tools#11493) Accept only left-clicks for adding annotations (mne-tools#11491) [BUG, MRG] Fix pial surface loading, logging in locate_ieeg (mne-tools#11489) [ENH] Added unit_role to add non-breaking space between magnitude and units (mne-tools#11469) MAINT: Fix CircleCI build (mne-tools#11488) [DOC] Updated decoding.SSD documentation and internal variable naming (mne-tools#11475) Typo fix (mne-tools#11485) ...

larsoner · 2024-11-18T14:14:09Z

I am a bit busy for the next two weeks but then should be able to come back to this!

larsoner · 2025-01-24T19:28:48Z

Okay two weeks turned into two months 😅 But I should be able to look next week

* upstream/main: (149 commits) FIX make_watershed_bem to handle missing talairach_with_skull.lta courtesy Freesurfer 8 (mne-tools#13172) ENH: Add upsampling for MEG helmet surface (mne-tools#13179) MAINT: Update code credit (mne-tools#13180) BUG: Fix bug with least-squares sphere fit (mne-tools#13178) fix EDF export (mne-tools#13174) fix typo (mne-tools#13171) [pre-commit.ci] pre-commit autoupdate (mne-tools#13164) Fix dev installation guide (mne-tools#13163) expose 'mode' for plotting dipole on brain (mne-tools#13162) turn dipole attrs into properties (mne-tools#13153) remove misformatted (and unused) crossref anchor (mne-tools#13155) doc: point to read_dipole (mne-tools#13149) [pre-commit.ci] pre-commit autoupdate (mne-tools#13152) BUG: Fix bug with not short-circuiting n_jobs=1 (mne-tools#13147) FIX: Missing coordinates.xml in MFF file (mne-tools#13148) FIX: Gracefully handle bad XML files in EGI reader (mne-tools#13145) Fixes for Latest IPython (9.0.1) (mne-tools#13146) Fix intersphinx (mne-tools#13143) BUG: Fix bug with parallel doc build (mne-tools#13140) [pre-commit.ci] pre-commit autoupdate (mne-tools#13141) ...

larsoner · 2025-04-04T18:23:52Z

Apologies for the embarassingly long delay on this one 🥵 Pushing some commits to make sure things are green, then I'll add the test files, etc!

larsoner

@julien-dubois-k okay I think I have it roughly where it could use another look from you to see if values are in the correct ranges, etc.!

larsoner · 2025-04-04T19:23:41Z

+        assert hbo_data.shape == hbr_data.shape == (shape[0] // 2, shape[1])
+        hbo_norm = np.nanmedian(np.linalg.norm(hbo_data, axis=-1))
+        hbr_norm = np.nanmedian(np.linalg.norm(hbr_data, axis=-1))
+        # TODO: Old file vs new file scaling, one is wrong!


Would be good to know if the numbers for the newer one are correct or not...

sorry, what do you mean?

The way the code works now the old test file and the new test file differ by several orders of magnitude (like 1e5) so I think there is uM vs M error scaling either in the file or in the code. Based on It looks like they should be closer to ~1e-6, right? If so then there is some bug in how we're reading the hbo/hbr values for the old file

larsoner · 2025-04-04T19:24:03Z

+        # TODO: Reasonable values here???
+        lims = dict(intensity=(1e4, 1e7), mean=(1e3, 1e4), variance=(1e5, 1e7))


I also don't know if these are reasonable values for the counts (intensity), mean (s), or variance (s**2)

these are reasonable if mean is in picoseconds and variance in ps^2.

ghost · 2025-04-07T15:53:51Z

-        fnirs_td_moments_amplitude=1e6,
+        fnirs_td_gated_amplitude=1.0,
+        fnirs_td_moments_intensity=1.0,
+        fnirs_td_moments_mean=1.0,


the values are in the range of nanoseconds, so this should be 1e-9 for mean and 1e-18 for variance maybe?

* upstream/main: (55 commits) doc: fix rendering typo rst docstr (mne-tools#13301) DOC: fix docstrs around layout functions (mne-tools#13300) MAINT: Fix doc build failure due to deprecation (mne-tools#13299) Birthday input cast to datetime.date (mne-tools#13284) DOC: fix missing space, use f-strings, structure->object (mne-tools#13291) [pre-commit.ci] pre-commit autoupdate (mne-tools#13290) ENH: channel_indices_by_type now has an exclude param (mne-tools#13293) Proj id and proj name access (mne-tools#13261) Fix: nearly invisible traces with spatial_colors=True (mne-tools#13286) [pre-commit.ci] pre-commit autoupdate (mne-tools#13283) Bump autofix-ci/action from 551dded8c6cc8a1054039c8bc0b8b48c51dfc6ef to 635ffb0c9798bd160680f18fd73371e355b85f27 in the actions group (mne-tools#13282) fix Maxwell bads filtering (mne-tools#13280) fix actionable linkcheck errors (mne-tools#13273) MAINT: Use radius keyword with PyVista tube (mne-tools#13277) BUG: Fix bug with simulating head pos and BEM (mne-tools#13276) [pre-commit.ci] pre-commit autoupdate (mne-tools#13274) MAINT: Update code credit (mne-tools#13267) Annotations extras (mne-tools#13228) Tidy up the directory reading (mne-tools#13268) FIX, DOC: Drop bad channel in 10_publication_figure.py (mne-tools#13266) ...

larsoner · 2025-06-26T19:47:08Z

Okay made some (again) overdue progress here! I think we need to look at / revise mne-tools/mne-nirs#586 next... see my comment mne-tools/mne-nirs#586 (comment)

jcrdubois · 2026-06-01T16:32:07Z

@larsoner I added changes from this stale branch on top of master, and fixed a couple of things, here #13938 Let's test this and get this merged soon!

larsoner · 2026-06-01T16:46:15Z

Closing for #13938

Zahra-M-Aghajan and others added 10 commits August 10, 2021 22:45

adding the new snirf data types to the constants

3f875d3

more places to add the data types and constants

cc92adc

adding constants for the allowed dataTypeLabels for the processed dat…

0d2fe87

…a type as outlined in the SNIRF specification document

updating the snirf reader to accept other data types: gated histogram…

21ecb90

…s, moments and processed (hbo/hbr)

setting the formatter line length

4491064

the reordering of the channels does not make much sense, need to inquire

dbdcebc

Merge remote-tracking branch 'upstream/main' into feature/TD-nirs_snirf

80de954

Merge remote-tracking branch 'upstream/main' into feature/TD-nirs_snirf

32c5496

MAINT: Simpler with .item

a35822a

WIP: Constants

c2c217c

larsoner mentioned this pull request Aug 21, 2022

Feature/td nirs snirf #9661

Open

larsoner added 9 commits August 21, 2022 20:54

FIX: Flake

ac52bc0

FIX: Consistent

da275f1

FIX: Missed

3986b96

FIX: Better code

ce8b3af

FIX: Scale

1244add

FIX: Missing

3944254

FIX: Flake

967dddd

FIX: Syntax

e97367d

Merge remote-tracking branch 'upstream/main' into feature/TD-nirs_snirf

4b963cd

larsoner added the fNIRS label Aug 23, 2022

rob-luke reviewed Aug 26, 2022

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Comment thread mne/defaults.py Outdated

JohnGriffiths mentioned this pull request Sep 6, 2022

fix fnirs channel name cropping in topomap combination #11138

Open

larsoner mentioned this pull request Feb 2, 2023

add ch_type and coils for eye-tracker data mne-tools/fiff-constants#39

Merged

larsoner added 4 commits March 1, 2023 12:46

FIX: shape

d26ff8a

FIX: Slash

f84fe27

FIX: Bad merge

50f3064

ghost reviewed Nov 12, 2024

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Comment thread mne/defaults.py Outdated

Comment thread mne/defaults.py Outdated

Comment thread mne/io/snirf/tests/test_snirf.py Outdated

JohnGriffiths mentioned this pull request Nov 13, 2024

initial draft of new TD-fNIRS KF2 example mne-tools/mne-nirs#586

Merged

3 tasks

larsoner modified the milestones: 1.9, 1.10 Dec 9, 2024

larsoner added 2 commits April 4, 2025 10:19

WIP: More constants

e9403d8

larsoner commented Apr 4, 2025

View reviewed changes

Comment thread mne/defaults.py

larsoner added 2 commits April 4, 2025 14:29

FIX: Caps

6ee5068

FIX: More

b2b3716

larsoner commented Apr 4, 2025

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ghost reviewed Apr 7, 2025

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larsoner added 2 commits June 26, 2025 14:30

FIX: Tests passing

636c42a

larsoner modified the milestones: 1.10, 1.11 Jun 26, 2025

larsoner mentioned this pull request Jun 26, 2025

ENH: Add extra needed fNIRS constants mne-tools/fiff-constants#45

Merged

larsoner mentioned this pull request Oct 22, 2025

Read Kernel Flow TD-fNIRS Moments Files mne-tools/mne-nirs#642

Open

Merge branch 'main' into feature/TD-nirs_snirf

8f8f957

larsoner removed this from the 1.11 milestone Nov 13, 2025

cbrnr removed request for cbrnr and dengemann April 23, 2026 10:33

This was referenced May 29, 2026

Feature/td nirs snirf jcrdubois/mne-python#1

Closed

Feature/td nirs snirf #13938

Open

larsoner closed this Jun 1, 2026

		# TODO: Reasonable values here???
		lims = dict(intensity=(1e4, 1e7), mean=(1e3, 1e4), variance=(1e5, 1e7))

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