amended `_write_electrodes_tsv` to exclude writing stim channels to electrodes.tsv #1023

scott-huberty · 2022-07-28T19:13:43Z

closes #1022

make tests and make pep passed on my local machine, fingers crossed!

…hey are not written to electrodes.tsv

welcome · 2022-07-28T19:13:46Z

Hello! 👋 Thanks for opening your first pull request here! ❤️ We will try to get back to you soon. 🚴🏽‍♂️

codecov · 2022-07-28T19:23:00Z

Codecov Report

Merging #1023 (8e0ac92) into main (7c08e3b) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main    #1023   +/-   ##
=======================================
  Coverage   95.17%   95.18%           
=======================================
  Files          25       25           
  Lines        3774     3777    +3     
=======================================
+ Hits         3592     3595    +3     
  Misses        182      182

Impacted Files	Coverage Δ
mne_bids/dig.py	`98.62% <100.00%> (+0.01%)`	⬆️

Help us with your feedback. Take ten seconds to tell us how you rate us.

hoechenberger · 2022-07-29T06:45:19Z

Great, can you add a test and a changelog entry please?

sappelhoff

Thanks! +1 to merge once the changelog entry is there

scott-huberty · 2022-07-29T12:53:33Z

Sure! I was going to add a test for this new behaviour using the 'test_egi.mff' in PR #1006 , but you're right it makes more sense to do it here.

Will add the test and update changelog now.

scott-huberty · 2022-07-29T18:56:30Z

I don't see a latest.inc file to add my changes to, should I add them whats_new.rst?

I'm not sure if my test is too convoluted, I was trying to test for two cases:

for the test file 'sample_audvis_trunc_raw.fif', only eeg channels (with electrodes) should be written to electrodes.tsv.
The warning that was identified in Add EGI as manufacturer #1006 that was getting raised during read_raw_bids "There are channels without locations", should no longer be getting raised, so if it does, the test will fail.

hoechenberger · 2022-07-29T18:54:57Z

mne_bids/tests/test_dig.py

+
+    # test 1
+    with open(bids_path.directory /
+              'sub-01_ses-01_acq-01_space-CapTrak_electrodes.tsv') as sidecar:


Should specify encoding='utf-8'

done, thanks for the tip!

hoechenberger · 2022-07-29T18:57:11Z

mne_bids/tests/test_dig.py

+    # test 2
+    with pytest.warns(RuntimeWarning) as record:
+        read_raw_bids(bids_path)
+        # list of warnings emitted by read_raw_bids


I appreciate your writing this test (looks like a lot of work!), but I don't think we need this one … we just need to ensure we're writing the correct stuff (which the previous test ensures); testing the reading operation again is, IMHO, overkill. I'd suggest to remove test 2.
@sappelhoff WDYT?

Yeah, I was wondering if it was too much ha. I can remove it.

mne_bids/tests/test_dig.py

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

mne_bids/tests/test_dig.py

hoechenberger · 2022-07-29T19:06:49Z

mne_bids/tests/test_dig.py

@@ -334,7 +334,7 @@ def test_electrodes_io(tmp_path):
    raw.pick_types(eeg=True, stim=True)  # we don't need meg channels
    bids_root = tmp_path / 'bids1'
    bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
-    os.makedirs(op.join(bids_root, 'sub-01', 'ses-01', 'eeg'), exist_ok=True)
+    (bids_root / 'sub-01' / 'ses-01' / 'eeg').mkdir(exist_ok=True)


Why do you need to create this directory manually, anyway..?

I'm not sure.. I was having a hard time understanding this, but was trying to follow the examples from the other tests in test.dig.py

write_raw_bids should create the directory tree, could you try without?

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

mscheltienne · 2022-07-29T19:16:13Z

And yes, for the changelog it's in whats_new.rst, thanks!

sappelhoff

@scott-huberty please also comment in #1028 with your full name, ORCID, and affiliation -- I'd like to add you there.

(@mscheltienne as well)

drammock · 2022-07-29T20:06:13Z

mne_bids/tests/test_dig.py

+        assert n_entries == len(
+            raw
+            .copy()
+            .pick_types(eeg=True)
+            .ch_names
+        )


seems my prior comment got lost: you should not need to do raw.copy() here. use raw.get_channel_types() and count the 'eeg's

Nice trick, @drammock!

awesome, thanks @drammock!

mne_bids/tests/test_dig.py

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

mscheltienne

I think those are the last points I see, + the encoding='utf-8' to be added as mentioned by Richard.

I hope this is the last change we need to add support for the EGI format!

doc/whats_new.rst

mne_bids/tests/test_dig.py

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

scott-huberty · 2022-07-29T22:33:34Z

@scott-huberty please also comment in #1028 with your full name, ORCID, and affiliation -- I'd like to add you there.

(@mscheltienne as well)

Thanks for that, @sappelhoff ! I think I commented in the right location of the zenodo json file.. Just Let me know if I commented in the wrong place.

welcome · 2022-07-30T08:12:46Z

🎉 Congrats on merging your first pull request! 🥳 Looking forward to seeing more from you in the future! 💪

hoechenberger · 2022-07-30T09:04:55Z

Thanks @scott-huberty!

scott-huberty · 2022-07-30T10:56:33Z

Thanks @scott-huberty!

Thanks everyone for the help!

amended mne_bids.dig._write_electrodes_tsv to skip stim channels so t…

290b24b

…hey are not written to electrodes.tsv

agramfort requested a review from hoechenberger July 28, 2022 19:28

sappelhoff approved these changes Jul 29, 2022

View reviewed changes

sappelhoff added this to the 0.11 milestone Jul 29, 2022

added test for properly writing to electrodes.tsv

5aafe00

hoechenberger reviewed Jul 29, 2022

View reviewed changes

mne_bids/tests/test_dig.py Outdated Show resolved Hide resolved

hoechenberger reviewed Jul 29, 2022

View reviewed changes

mne_bids/tests/test_dig.py Outdated Show resolved Hide resolved

Update mne_bids/tests/test_dig.py

463f2cb

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

hoechenberger reviewed Jul 29, 2022

View reviewed changes

mne_bids/tests/test_dig.py Outdated Show resolved Hide resolved

hoechenberger reviewed Jul 29, 2022

View reviewed changes

scott-huberty and others added 2 commits July 29, 2022 15:13

Update mne_bids/tests/test_dig.py

bc07f85

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

Update mne_bids/tests/test_dig.py

b8f0537

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

scott-huberty added 2 commits July 29, 2022 15:34

removed second test from test_electrodes_io

7d1bd5e

updated change log

51d15b5

sappelhoff reviewed Jul 29, 2022

View reviewed changes

drammock reviewed Jul 29, 2022

View reviewed changes

updated test_electrodes_io per reviewer comments

18ec217

mscheltienne reviewed Jul 29, 2022

View reviewed changes

mne_bids/tests/test_dig.py Outdated Show resolved Hide resolved

Update mne_bids/tests/test_dig.py

7d62acb

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

mscheltienne reviewed Jul 29, 2022

View reviewed changes

doc/whats_new.rst Show resolved Hide resolved

mne_bids/tests/test_dig.py Outdated Show resolved Hide resolved

scott-huberty and others added 3 commits July 29, 2022 18:04

Update doc/whats_new.rst

e2d3e09

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

Update mne_bids/tests/test_dig.py

eddde80

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

specifying encoding=utf-8 in per reviewer suggestion

da4c198

hoechenberger added 2 commits July 30, 2022 09:49

Rework test a little

1fab1e5

Merge branch 'main' into electrodes_dev

8e0ac92

hoechenberger enabled auto-merge (squash) July 30, 2022 08:00

hoechenberger merged commit fc28eae into mne-tools:main Jul 30, 2022

mscheltienne mentioned this pull request Jul 30, 2022

[MRG, DOC] Fix whats_new.rst link #1032

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

amended `_write_electrodes_tsv` to exclude writing stim channels to electrodes.tsv #1023

amended `_write_electrodes_tsv` to exclude writing stim channels to electrodes.tsv #1023

scott-huberty commented Jul 28, 2022

welcome bot commented Jul 28, 2022

codecov bot commented Jul 28, 2022 •

edited

hoechenberger commented Jul 29, 2022

sappelhoff left a comment

scott-huberty commented Jul 29, 2022

scott-huberty commented Jul 29, 2022

hoechenberger Jul 29, 2022

scott-huberty Jul 29, 2022

hoechenberger Jul 29, 2022

scott-huberty Jul 29, 2022

hoechenberger Jul 29, 2022

scott-huberty Jul 29, 2022

mscheltienne Jul 29, 2022 •

edited

mscheltienne commented Jul 29, 2022

sappelhoff left a comment •

edited

drammock Jul 29, 2022

hoechenberger Jul 29, 2022

scott-huberty Jul 29, 2022

mscheltienne left a comment

scott-huberty commented Jul 29, 2022

welcome bot commented Jul 30, 2022

hoechenberger commented Jul 30, 2022

scott-huberty commented Jul 30, 2022

amended _write_electrodes_tsv to exclude writing stim channels to electrodes.tsv #1023

amended _write_electrodes_tsv to exclude writing stim channels to electrodes.tsv #1023

Conversation

scott-huberty commented Jul 28, 2022

welcome bot commented Jul 28, 2022

codecov bot commented Jul 28, 2022 • edited

Codecov Report

hoechenberger commented Jul 29, 2022

sappelhoff left a comment

Choose a reason for hiding this comment

scott-huberty commented Jul 29, 2022

scott-huberty commented Jul 29, 2022

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

mscheltienne Jul 29, 2022 • edited

Choose a reason for hiding this comment

mscheltienne commented Jul 29, 2022

sappelhoff left a comment • edited

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

mscheltienne left a comment

Choose a reason for hiding this comment

scott-huberty commented Jul 29, 2022

welcome bot commented Jul 30, 2022

hoechenberger commented Jul 30, 2022

scott-huberty commented Jul 30, 2022

amended `_write_electrodes_tsv` to exclude writing stim channels to electrodes.tsv #1023

amended `_write_electrodes_tsv` to exclude writing stim channels to electrodes.tsv #1023

codecov bot commented Jul 28, 2022 •

edited

mscheltienne Jul 29, 2022 •

edited

sappelhoff left a comment •

edited