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In-database BIDS file information - #1443

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MaximeBICMTL:bids-info
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In-database BIDS file information#1443
MaximeBICMTL wants to merge 5 commits into
aces:mainfrom
MaximeBICMTL:bids-info

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@MaximeBICMTL MaximeBICMTL commented Jun 17, 2026

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This PR implements aces/Loris#11169 for the LORIS BIDS MRI and EEG importer. Code-wide, this PR improves the BIDS importer by refactoring BidsImportEnv into a more feature-complete BidsImporter class. However, the code for actual BIDS registration also complexifies the importer quite a bit, and simplifying it would require a large (but desirable) refactor of the BIDS importer (specifically create a common factorization for all BIDS file imports), which is outside of the scope of this PR. Integration tests are nonetheless improved in this PR to ensure that everything works as expected and continues to do so in the future.

BIDS importer design

  • Rename BidsImportEnv to BidsImporter.
  • BidsImporter is the central object for BIDS import, which contains:
    • Arguments passed to the BIDS importer.
    • State of the BIDS importer (successed/skipped/failed files).
    • Custom importers hooked to the LORIS BIDS importer.

Open design questions

  • Should the BIDS dataset tables be used for the assembly BIDS (IMO yes).
  • Store how each BIDS file was added to LORIS (importer/converter)?
  • Add a script to generate BIDS dataset/files table from an already-imported BIDS dataset present on the file system?
  • Many others!

@github-actions github-actions Bot added the Language: Python Issue or PR related to the Python codebase label Jun 17, 2026
@github-actions github-actions Bot added the Package: BIDS importer PR or issue related to the BIDS importer label Jun 17, 2026
@MaximeBICMTL
MaximeBICMTL force-pushed the bids-info branch 3 times, most recently from b1400ce to 40953c6 Compare June 22, 2026 13:30
@MaximeBICMTL MaximeBICMTL added this to the 30.0.0 milestone Jun 22, 2026
@MaximeBICMTL
MaximeBICMTL force-pushed the bids-info branch 4 times, most recently from 7ebbfbe to febe169 Compare June 23, 2026 09:39
@MaximeBICMTL MaximeBICMTL added Complexity: Complex Issue or PR that requires a great effort to implement, review, or test Category: Feature Issue or PR that aims to introduce a new feature labels Aug 11, 2026
@MaximeBICMTL
MaximeBICMTL force-pushed the bids-info branch 2 times, most recently from d9d071d to bec013b Compare August 13, 2026 13:06
@maximemulder
maximemulder marked this pull request as ready for review August 13, 2026 13:06
@MaximeBICMTL
MaximeBICMTL requested review from cmadjar and ridz1208 and removed request for cmadjar and ridz1208 August 13, 2026 13:23
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Category: Feature Issue or PR that aims to introduce a new feature Complexity: Complex Issue or PR that requires a great effort to implement, review, or test Language: Python Issue or PR related to the Python codebase Package: BIDS importer PR or issue related to the BIDS importer

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