bids_filter null values broken by fmriprep.config

[bpinsard]

What version of fMRIPrep are you using?

20.1.0

What kind of installation are you using? Containers (Singularity, Docker), or "bare-metal"?

Singularity pulled from dockerhub.

What is the exact command-line you used?

<place your command line here>

NA

Have you checked that your inputs are BIDS valid?

NA

Did fMRIPrep generate the visual report for this particular subject? If yes, could you share it?

NA

Can you find some traces of the error reported in the visual report (at the bottom) or in crashfiles?

NA

Are you reusing previously computed results (e.g., FreeSurfer, Anatomical derivatives, work directory of previous run)?

NA

fMRIPrep log

If you have access to the output logged by fMRIPrep, please make sure to attach it as a text file to this issue.

NA

BUG

I am using a bids-filter file containing:

{
  "t1w": {
    "reconstruction": null,
    "acquisition": null
  }
}

But after runnning fMRIPrep, in the config file the corresponding section is empty:

[execution.bids_filters.T1w]

I tested toml.dumps with a similar dict, and it seems that it does not dump any dict entry with value None.

In [3]: toml.dumps(dict(t1w=dict(acquisition=None)))                                       
Out[3]: '[t1w]\n'                                                                        
                                                                                          
In [4]: toml.dumps(dict(t1w=dict(acquisition=1)))                                                  
Out[4]: '[t1w]\nacquisition = 1\n'                                                                   
                                                                                        

I don't know if this is a toml issue, or should we write an encoder/decoder that allows None/null values.

The other option would be to replace None with pybids.value (as it is done for bids.layout.Query.ANY) which dumps with toml:

In [8]: toml.dumps(dict(t1w=dict(acquisition=bids.layout.Query.NONE)))
Out[8]: '[t1w]\nacquisition = "<Query.NONE: 1>"\n'

There might be other cases when storing null value is significant.

[bpinsard]

might be worth adding a dump-load-compare test of a config with a bids-filters with edge cases such that one.