Add only existing jsonfiles to jsonfiles and make it set #215
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…g nonexistent jsonfiles)
| @@ -308,6 +308,8 @@ def bidscoiner_plugin(session: Path, bidsmap: dict, bidsses: Path) -> Union[None | |||
| if bcoin.run_command(command): | |||
| if not list(outfolder.glob(f"{bidsname}.*nii*")): continue | |||
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| jsonfiles.update(outfolder.glob(f"{bidsname}.json")) # add existing created json files: bidsname.json | |||
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This line should also be added right after the physio2tsv conversion above (i.e. after line 295)
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Thanks, I have never come across this myself, but it looks like a clean solution. And I agree, |
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Sometimes is the return code of running dcm2niix success even though no nii files, therefore no json files were produced. This means that jsonfiles will need to remove <outfolder/bidsname.json> as it doesn't exist.
This code changes jsonfiles to set and only adds jsonfiles if they exist, meaning no need of removing nonexistent jsonfiles.
Maybe continue can be added not only for if return code is not success, but also if no nii files are produced?