[ENH] add option to include derivatives in BIDSDataGrabber #2815
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Codecov Report
@@ Coverage Diff @@
## master #2815 +/- ##
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+ Coverage 67.46% 67.48% +0.01%
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Files 341 341
Lines 43331 43342 +11
Branches 5371 5374 +3
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+ Hits 29235 29250 +15
+ Misses 13396 13390 -6
- Partials 700 702 +2
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@jdkent Sorry, I haven't had time to really think this through. Especially given that it may conflict with (I haven't checked) @adelavega's #2737 (which also needs to merge master), I think we should put this off to next release. |
| exclude = None | ||
| if self.inputs.strict: | ||
| exclude = ['derivatives/', 'code/', 'sourcedata/'] | ||
| layout = BIDSLayout(self.inputs.base_dir, exclude=exclude) | ||
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| if pybids_ver < version.parse('0.5'): |
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Maybe you can include something like this in my PR? My PR is more general update to 0.7, and includes some extra functionality / updates, in addition to allowing for derivatives. I just hadn't merged because I'm waiting for pybids 0.7 release.
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Although now that I think about it, I wouldn't worry too much about backwards compatibility. I would make 0.7 the hard requirement. The default behavior of my PR is to only look in the core BIDS folder, but you can optionally ask it to look in /derivatives or add extra paths.
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Closing in favor of #2737. If further changes are needed, please open a new PR. (I think trying to merge and salvage a usable commit history from this one is probably not worth it.) |
Summary
The behavior of pybids changed from
0.5.*to0.6.*such that the derivatives domain is not included in the default search pattern.Fixes #2814
This pull request is partially overlapping with #2737
List of changes proposed in this PR (pull-request)
domainsoption in BIDSDataGrabber for user to select what domains should be used for indexing filesAcknowledgment