file writing functionality

[tyarkoni]

One suggestion that has come up multiple times at the BIDS hackathon is to add functionality to grabbids for writing out files. The practical benefit of this is that it would allow grabbids to function as a BIDS conversion utility from almost any file structure that contains the mandatory keywords (subject, run, etc.) in the filenames. I.e., a user could define a JSON config file that picks out the BIDS-defined keywords within their existing file structure, and then call something like Layout.write_project(output_path, symbolic_links=True) to rewrite the entire existing project in BIDS-compatible form. We could allow options for copying, moving, or symlinking files.

It's unlikely that this would get users 100% of the way to BIDS compliance--e.g., because there's no generic way to rewrite event files, metadata, etc., but it might ease the process sufficiently that many people who are otherwise on the fence make the jump.

[tyarkoni]

paging @qmac

[tyarkoni]

As of grabbles/grabbit#32, grabbit now supports file writing via a new WritableLayout extension class that's a drop-in replacement for Layout. The only thing left to do is define a list of patterns in pybids/grabbids that describe the valid rules for outputting BIDS files (for format, see examples in this test). This then replaces a potentially large amount of explicit logic, and allows fairly powerful mappings between non-BIDS file-based organization schemes and BIDS.

[parth-verma]

Is this issue still open? If yes, I would love to work on it with a little bit of guidance from the developers (newbie here).