Update handling of external dwi_dir
#86
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Previously, if dwi_dir was passed, a naming scheme as assumed. Rather than hardcode the naming scheme, this change passes dwi_dir through to generate_inputs, which should enable different name schemes to be picked up. Bonus, it suppresses the message of not being able to find files, unless it actually is unable to find data in the provided paths. By default, if dwi_dir is not provided, it falls back on bids_dir.
Previously, the usage of `wildcards` was vast in the config file, allowing for wildcards for all sorts of entities. This PR constrains the wildcards to just subject, session, and run (can consider others in the future, but these make the most sense at the moment). Dwi filters are constrained to be in the "T1w" space, as we assume dwi processing should be performed in the same space as T1w. Alternatively, can consider "orig" space as well, but will need to think about to handle transformations to the T1w in that case. If multiple entities are found (e.g. "res"), Snakebids will throw an error reflecting the files found and suggest to the user to make use of the `--filter` option to constrain the files.
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Proposed changes
Resolves #84 - previously when
dwi_dirwas provided, the originalbids_diris still used to search for dwi data, resulting in a message regarding the inability to find files. This PR changes this behaviour, by splitting off the search for dwi data into a separategenerate_inputscall, falling back tobids_dirifdwi_diris not provided. By doing this, the message will only appear if there actually is no data that can be found. To that end, also added in thepybidsdbfunctionality, for bothbids_diranddwi_dir(if provided).Additionally, there were many wildcards in the config previously, allowing potential expansion over a number of different entities (e.g. res, run, acquisition, etc). Instead this PR falls back to only allowing subject, session, and runs as wildcards, which I think makes a little more sense. In doing so, it allows for flexibility in the naming schemes to be picked up (e.g. prepdwi vs snakedwi) and in the event multiple inputs are found, an error is raised, suggesting to the end-user to make use of the
--filterflag to constrain their selection. This also eliminates the need to hardcode the naming scheme of dwi that was done previously (e.g.desc=preprocordesc='eddy', res='orig'.Types of changes
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