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Add support for "configuration" files #280

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smoia opened this issue Jul 30, 2020 · 1 comment
Open
4 tasks

Add support for "configuration" files #280

smoia opened this issue Jul 30, 2020 · 1 comment
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Enhancement New feature or request

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@smoia
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smoia commented Jul 30, 2020

This moves both in favour of an easier management of the CLI and in favour of a quicker reusability of the pipeline,
also letting the centres that are interested (BCBL, NW, FIU, ...) to have a prepared setup to run phys2bids.
The idea is to be able to call phys2bids either with the commands that we know, or with a flag --config followed by a configuration file that gives all the arguments to phys2bids.
It could be a txt file, a yaml or json file, or simply a CLI bump to a file.
We should also save this file, so that further runs of phys2bids can use it to reproduce the same pipeline.

Possible Implementation

  • Decide the type of file for the configuration (yaml or txt would be a good option!)
  • Add a parser argument to accept it
  • Add a function that reads the config file, but doesn't overwrite the options given as input in the CLI
  • Add a function to export this configuration file
@smoia smoia added the Enhancement New feature or request label Jul 30, 2020
@smoia smoia added this to the phys2bids second semester 2020 milestone Jul 30, 2020
@vinferrer
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  • We could actually put this config file to the folder code/conversion both when is introduced by the user and when the flags are manually inputted. This way a person can call manually phys2bids flags and then reused the generated config files for other recordings so they only have to change a few parameters

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