[WIP] Tests #27
[WIP] Tests #27
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Looks like a great start. Thanks @teonbrooks
yes, I think we can use a pure python validator indeed. See here: https://github.com/INCF/pybids/blob/master/bids/grabbids/bids_validator.py
It doesn't have the MEG part though. I could update it once I'm done with the validator on INCF. I merged the other PR so you can focus on the tests in this PR. You will need to rebase :)
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| from .bids_meg import raw_to_bids | |||
| from .bids_meg import _mkdir_p | |||
| from .meg_bids import raw_to_bids | |||
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good call from the linguist ;)
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| def test_kit(): |
this would be great to have. what I will do for now if make the tests for the four different meg types, and then we can add the validation steps to those tests. I think that would be sufficient. |
@jasmainak, anything I can do to help with the validator? |
- Add default value for unlisted channel types - Fix support for BTi data - Fix overwrite for non-FIF files
| eog='EOG', ecg='ECG', misc='MISC', ref_meg='REFMEG') | ||
| map_desc = dict(grad='Gradiometer', mag='Magnetometer', | ||
| map_desc = defaultdict(lambda: 'Other type of channel') |
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The spec has a restricted list of channel types but I wonder if there is a way to preserve some info we extract to put in the description. e.g. resp is a channel type in the BTi data but that info would be lost
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hmm ... you can always add it in the description, but it's true that "other" is no longer an available option. Perhaps we should update the MEG draft for that? Although I'd rather not have the draft updated at this point so we can write the software (validator etc.) with what we have
Yes, that sounds like a great plan! |
I guess it's mostly a matter of copying the regular expressions and json schemas from the pull request on the INCF website to |
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@teonbrooks would you mind adding a |
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yeah, I think we can merge these tests and changes so that we can address @choldgraf PR #28 to generalize the reader. I know that I have modded some code here so that PR will need to rebase and resolve the conflicts |
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Done, thanks @teonbrooks :) |
building from, closes #23, closes #5.
I am adding tests for all four MEG systems since we have test data for them all. Should our tests compare itself to the validator? I think there is supposed to be a python bids validator. Since we are utilizing already tested mne readers for the conversion tool, we shouldn't need to validate them. We need to make sure filenames are correct.
Possible addition: anonymize kwarg in
raw_to_bids. We have a function already that does this, we can expose in the conversion step.