0- vs 1-indexing the run keyword in use_heuristic()

[rmarkello]

In #76 (comment) a brief discussion was started about whether the run keyword should be 0- or 1-indexed when users provide a heuristic to convert their data to BIDS format. We are currently using a 0-indexing approach; I personally think a 1-indexing approach makes more sense here, but am open to discussion on this point!

@smoia found a relevant portion of the BIDS spec that touches on this, but the spec is not prescriptive on this point. I'm happy to hear others thoughts and go about issuing a change if it's decided that's warranted!

[smoia]

I see that actually we were talking about two different things.
I thought you were referring to padding - that's the only thing the specs refer to.
I didn't find anything related to 0- or 1- indexing, although most of the examples are 1-indexed.

As we don't support multiple files or multiscan files yet, if we want to implement this we should also think about a way to check that then different calls of phys2bids respect the overall indexing, i.e. if the user adopts a 0-indexing and has -0 -1 -2 we don't overwrite -1.
(If it's not clear let me know).

[smoia]

@rmarkello let's get back to this issue. Shall we agree on suggesting the user to adopt a 1-indexed run keyword, and remain agnostic about it?

[rmarkello]

I am for starting at run-01 and indexing up from there (i.e., run-00 should not be allowed), yes!

[smoia]

Do you think we need to add something to the code as it is now to accommodate for this decision?

[rmarkello]

It looks like there are a few instances in the heuristic files provided with phys2bids where run-00 is used:

phys2bids/phys2bids/heuristics/heur_test_acq.py

Lines 19 to 22 in 3dc8c8a

	if fnmatch.fnmatchcase(physinfo, '*samefreq*'):
	task = 'test'
	run = '00'
	rec = 'biopac'

phys2bids/phys2bids/heuristics/heur_tutorial.py

Lines 19 to 22 in 3dc8c8a

	if fnmatch.fnmatchcase(physinfo, '*tutorial*'):
	task = 'test'
	run = '00'
	rec = 'labchart'

These heuristics and all relevant tests / documentation would need to be updated to reflect this decision.

[smoia]

That's right - actually, those values are just an example. We can definitely change them without any big impact!