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childmindresearch / bids2table

Efficiently index large-scale BIDS neuroimaging datasets and derivatives
https://childmindresearch.github.io/bids2table/
MIT License
13 stars 5 forks source link

Improve sidecar handling #10

Closed clane9 closed 1 year ago

clane9 commented 1 year ago

Some datasets such as those generated by MRIQC create isolated JSON sidecars, which would have previously been skipped. Now we try to tighten the filtering to only exclude sidecars that are associated to other data files.

Fix handling of sidecars that are shared across all subjects and sessions.

Add dataset_type to output table.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 95.83% and project coverage change: +0.19 :tada:

Comparison is base (982cca0) 89.02% compared to head (f4f3006) 89.22%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #10 +/- ## ========================================== + Coverage 89.02% 89.22% +0.19% ========================================== Files 10 10 Lines 419 436 +17 ========================================== + Hits 373 389 +16 - Misses 46 47 +1 ``` | [Impacted Files](https://app.codecov.io/gh/cmi-dair/bids2table/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmi-dair) | Coverage Δ | | |---|---|---| | [bids2table/extractors/dataset.py](https://app.codecov.io/gh/cmi-dair/bids2table/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmi-dair#diff-YmlkczJ0YWJsZS9leHRyYWN0b3JzL2RhdGFzZXQucHk=) | `89.58% <ø> (ø)` | | | [bids2table/extractors/sidecar.py](https://app.codecov.io/gh/cmi-dair/bids2table/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmi-dair#diff-YmlkczJ0YWJsZS9leHRyYWN0b3JzL3NpZGVjYXIucHk=) | `91.42% <92.85%> (+0.51%)` | :arrow_up: | | [bids2table/\_bids2table.py](https://app.codecov.io/gh/cmi-dair/bids2table/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmi-dair#diff-YmlkczJ0YWJsZS9fYmlkczJ0YWJsZS5weQ==) | `90.00% <100.00%> (+0.52%)` | :arrow_up: | | [bids2table/extractors/\_inheritance.py](https://app.codecov.io/gh/cmi-dair/bids2table/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmi-dair#diff-YmlkczJ0YWJsZS9leHRyYWN0b3JzL19pbmhlcml0YW5jZS5weQ==) | `88.23% <100.00%> (ø)` | | | [bids2table/extractors/bids.py](https://app.codecov.io/gh/cmi-dair/bids2table/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmi-dair#diff-YmlkczJ0YWJsZS9leHRyYWN0b3JzL2JpZHMucHk=) | `89.65% <100.00%> (+0.76%)` | :arrow_up: | | [bids2table/extractors/entities.py](https://app.codecov.io/gh/cmi-dair/bids2table/pull/10?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cmi-dair#diff-YmlkczJ0YWJsZS9leHRyYWN0b3JzL2VudGl0aWVzLnB5) | `95.42% <100.00%> (ø)` | |

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