Implement Bids Spec files #324
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pvandyken
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In fact, this PR does introduce a slight behaviour change. Previously, if bids(root=".", subject="001") == "sub-001/sub-001"Now, the bids(root=".", subject="001") == "./sub-001/sub-001"Practically speaking, this shouldn't make much of a difference, as the paths are still canonically the same (It got me in some of my tests, but they are more strict about paths being exactly correct). But I think this change is more correct than previous behaviour. |
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Add spec files and getters
Bids() is refactored to use the new bids specs, paving the way for future customizable bids functions, plus speeds it up 2-3 fold. Also adds a brand new test suite.
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This is the first out of two PRs for the resolution of #245. Here, we add define the spec file and add a
0.0.0file to represent the bids function as it's been until now. The api does not change at all here, but the bids function has been refactored to use the spec.I also added an extensive test suite for the bids function.
The spec
The spec takes the following form (in yaml)
The order of entries determines the order entities will be placed in by the bids function.
datatype,suffix,extension, andprefixare considered nonstandard entities and must not be specified in the config. Unrecognized entities are, by default, placed at the end of the path before the suffix. However, at most one entry in the spec may be specified as:This indicates a placeholder determining the insertion point of unrecognized entities.
Currently, no validation of the above specifications is enforced. The
bids()function is hard-coded to use the0.0.0spec, which I already know is valid. In the future, when we support custom spec files, we will need to implement validation.