Include ecog and seeg #281

chapochn · 2022-07-20T00:08:00Z

the function get_rejection_threshold now also works when the data is ecog or seeg

get_rejection_threshold

chapochn · 2022-07-20T02:55:24Z

I don't really understand the error in the checks

chapochn · 2022-07-20T15:15:39Z

related to #276 and #198

jasmainak · 2022-07-20T19:06:02Z

the error is unrelated. Maybe @hoechenberger or @sappelhoff knows what's up?

autoreject/autoreject.py

sappelhoff · 2022-07-20T19:12:38Z

No idea ... I was hoping this was a temporary issue. But it seems to persist. Somebody will have to dig into this :-)

hoechenberger · 2022-07-20T21:19:38Z

Seems like yet another issue with OpenNeuro. We'll have to
file a bug report...

sappelhoff · 2022-07-21T06:18:42Z

@chapochn would you mind filing a bug report about this on https://github.com/OpenNeuroOrg/openneuro/ ?

chapochn · 2022-07-21T18:22:21Z

@sappelhoff I have no experience with OpenNeuro.
This is the error from circleci:


Sphinx-Gallery successfully executed 6 out of 7 files subselected by:

    gallery_conf["filename_pattern"] = '/plot'
    gallery_conf["ignore_pattern"]   = '__init__\\.py'

after excluding 0 files that had previously been run (based on MD5).


Traceback (most recent call last):
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/sphinx/cmd/build.py", line 276, in build_main
    app.build(args.force_all, filenames)
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/sphinx/application.py", line 331, in build
    self.events.emit('build-finished', None)
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/sphinx/events.py", line 94, in emit
    results.append(listener.handler(self.app, *args))
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/sphinx_gallery/gen_gallery.py", line 732, in summarize_failing_examples
    raise ExtensionError(fail_message)
sphinx.errors.ExtensionError: Here is a summary of the problems encountered when running the examples

Unexpected failing examples:
/home/circleci/project/examples/plot_visualize_bad_epochs.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/project/examples/plot_visualize_bad_epochs.py", line 33, in <module>
    openneuro.download(dataset=dataset, target_dir=target_dir,
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/openneuro/download.py", line 684, in download
    asyncio.run(_download_files(**kwargs))
  File "/opt/circleci/.pyenv/versions/3.9.7/lib/python3.9/asyncio/runners.py", line 44, in run
    return loop.run_until_complete(main)
  File "/opt/circleci/.pyenv/versions/3.9.7/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
    return future.result()
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/openneuro/download.py", line 468, in _download_files
    await asyncio.gather(*download_tasks)
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/openneuro/download.py", line 330, in _download_file
    raise RuntimeError(
RuntimeError: Error 404 when trying to download /home/circleci/project/autoreject/../examples/ds000117/dataset_description.json from https://s3.amazonaws.com/openneuro.org/ds000117/dataset_description.json?versionId=vbCEkbZtCL26q._PCPmrCJK_KngbQ_dT


-------------------------------------------------------------------------------

Extension error:
Here is a summary of the problems encountered when running the examples

Unexpected failing examples:
/home/circleci/project/examples/plot_visualize_bad_epochs.py failed leaving traceback:
Traceback (most recent call last):
  File "/home/circleci/project/examples/plot_visualize_bad_epochs.py", line 33, in <module>
    openneuro.download(dataset=dataset, target_dir=target_dir,
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/openneuro/download.py", line 684, in download
    asyncio.run(_download_files(**kwargs))
  File "/opt/circleci/.pyenv/versions/3.9.7/lib/python3.9/asyncio/runners.py", line 44, in run
    return loop.run_until_complete(main)
  File "/opt/circleci/.pyenv/versions/3.9.7/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
    return future.result()
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/openneuro/download.py", line 468, in _download_files
    await asyncio.gather(*download_tasks)
  File "/home/circleci/autoreject_env/lib/python3.9/site-packages/openneuro/download.py", line 330, in _download_file
    raise RuntimeError(
RuntimeError: Error 404 when trying to download /home/circleci/project/autoreject/../examples/ds000117/dataset_description.json from https://s3.amazonaws.com/openneuro.org/ds000117/dataset_description.json?versionId=vbCEkbZtCL26q._PCPmrCJK_KngbQ_dT


-------------------------------------------------------------------------------
make: *** [Makefile:20: html] Error 2

Exited with code exit status 2

CircleCI received exit code 2

What is the command that is causing the error?

hoechenberger · 2022-07-21T19:14:09Z

I've field a bug report at OpenNeuroOrg/openneuro#2635

sappelhoff · 2022-07-21T20:02:21Z

and apparently already solved -- I'll restart CI

chapochn · 2022-07-22T19:11:32Z

I added 2 tests, but I can see that some checks failed. I'm not sure how to see the error, do I need to be able to access Azure? I don't seem to have access. Please let me know.

sappelhoff · 2022-07-22T20:18:19Z

yeah, I need to sign in with my microsoft account -- and I don't have access to the logs:

autoreject/tests/test_autoreject.py

jasmainak · 2022-07-23T03:21:38Z

Can you just change the channel type of a regular EEG channel so as to not add a dependency on mne_bids for the test? There is nothing specific about sEEG in your test at the moment.

autoreject/tests/test_autoreject.py

jasmainak · 2022-07-23T22:05:04Z

autoreject/tests/test_autoreject.py

@@ -364,3 +364,60 @@ def test_fnirs():
    assert reject["hbo"] < 0.001  # This is a very high value as sanity check
    assert reject["hbr"] < 0.001
    assert reject["hbr"] > 0.0
+
+
+def test_ecog():


we follow PEP 257. See how docstrings should be formatted: https://peps.python.org/pep-0257/

not sure to which place you're referring to, but I changed something, see in the next commit

see: "Multi-line docstrings consist of a summary line just like a one-line docstring, followed by a blank line, followed by a more elaborate description."

ok thanks, pushed a new version

slightly changed docstring

jasmainak · 2022-07-23T22:29:29Z

autoreject/tests/test_autoreject.py

+        epochs.load_data()
+        n1 = len(epochs)
+        reject = get_rejection_threshold(epochs)
+        print(reject)


Suggested change

print(reject)

no print statements in tests ...

ok, I copied that from a test that was already there

jasmainak · 2022-07-23T22:29:51Z

Can you update whats_new.rst so we can give you credit in the next release?

chapochn · 2022-07-23T22:41:19Z

ok, updated changelog, thanks for suggesting!

jasmainak · 2022-07-23T22:43:22Z

looks like you need to rebase with respect to the latest master branch:

$ git fetch upstream master:master
$ git rebase master
$ git push -f origin include-ecog

chapochn · 2022-07-23T23:11:19Z

Should be ok now

jasmainak · 2022-07-23T23:24:29Z

I still can't merge ...

jasmainak · 2022-07-23T23:25:37Z

I went ahead and squashed your commits. Thanks @chapochn ! 🥳

chapochn · 2022-07-25T17:18:08Z

Great, thank you!

chapochn added 2 commits July 19, 2022 19:54

added the option of having ecog or seeg channel for the function

b5a9c0b

get_rejection_threshold

updated doc

79312ab

jasmainak reviewed Jul 20, 2022

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autoreject/autoreject.py Show resolved Hide resolved

hoechenberger mentioned this pull request Jul 21, 2022

S3 URL returned for ds000117 is incorrect OpenNeuroOrg/openneuro#2635

Closed

added test for ECoG and sEEG

9b9f1b4

jasmainak reviewed Jul 23, 2022

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autoreject/tests/test_autoreject.py Outdated Show resolved Hide resolved

modified ecog test to not use new imports

076ea78

jasmainak reviewed Jul 23, 2022

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autoreject/tests/test_autoreject.py Outdated Show resolved Hide resolved

jasmainak reviewed Jul 23, 2022

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chapochn added 3 commits July 23, 2022 18:14

combined seeg and ecog test function into one

3f4cc9b

slightly changed docstring

added blank line at the end of file

92a009b

updated docstring

26e0624

jasmainak reviewed Jul 23, 2022

View reviewed changes

chapochn added 2 commits July 23, 2022 18:31

removed print from test

adb1498

updated changelog

ccc576e

Merge branch 'master' into include-ecog

23437c8

jasmainak merged commit 653160a into autoreject:master Jul 23, 2022

chapochn deleted the include-ecog branch July 25, 2022 17:32

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Include ecog and seeg #281

Include ecog and seeg #281

chapochn commented Jul 20, 2022

chapochn commented Jul 20, 2022 •

edited

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chapochn commented Jul 25, 2022

Include ecog and seeg #281

Include ecog and seeg #281

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chapochn commented Jul 20, 2022

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