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brain-microstructure-exploration-tools / abcd-microstructure-pipelines

Processing pipelines to extract brain microstructure from ABCD Study dMRI
Apache License 2.0
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add more tests for brain masking #26

Closed ebrahimebrahim closed 4 months ago

ebrahimebrahim commented 5 months ago

Follow-up to #19 to get more test coverage and set precedent for how to test IO steps

See comments in #25

allemangD commented 5 months ago

An important thing I want to include here is to test the promises we're making about not clobbering input files and respecting file structure. We can just do this in a temp dir with randomized data.

On mocking - I agree that most tests don't need to run HD-BET. We should probably have at least one test that does run the full pipeline end-to-end, including HD-BET, on at least one case to be sure we get sensible output. I'm not sure what steps will be required to allow mocking just the HD-BET component... will look into how pytest handles this for plain function calls.