feat: NDA Experimental ID from tsv#47
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WillForan wants to merge 2 commits into
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new argument to specify a tsv with ExperimentID and Pattern columns if Pattern is matched, use paired ExperimentID for image03 input file row json side car ExperimentID value used over pattern match if it exists includes unit and integratoin test
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I think the current
ExperimentIDin json sidecar solution is sufficient. But for our dataset, I do not want to update existing json file modification timestamps. I suspect this might be an unusual case not worth the extra code maintenance burden, but leaving here just in case. (Maybe if ExperimentID needs to be assigned to other files w/o a sidecar?)Similar to #37, this provides a new argument
--experimentid_tsv EXPERIMENTID_TSVto specify a tsv withExperimentIDandPatterncolumns.if
filematchesPattern, the paired ExperimentID is added to the image03 dict.When it exists, the JSON side car
ExperimentIDvalue is used instead of a pattern match.Most of the changes are in their own new file
bids2nda/experiment_id.pyand tests in tests/test_eid.py.The PR includes unit and integration test.
The integration test uses
nibabel.data_dir / "standard.nii.gz"for input. The files hasunknownfor the xyzt measurement.units_dictwas updated to handle this.