Improve consistency in core class about brainglobe-atlasapi

[FedeClaudi]

think that it would be good not to have tons of duplicated methods to deal with this; we could probably have a decorator that parses the input, check if value is a string, an int, a list of strings, or a list of ints, prepend a conversion if required, iterates if required, but then applies always a single method.
In the backend method we should always use either acronyms or regions ids - I would go for ids.

I like this. Definitively don't duplicate for list vs single items, methods should be flexible enough to deal with both.
I don't have any experience with decorators though so not sure how best to implement this.

If the region is the returned value (eg, get_region_name_from_coords(coords)), I would not duplicate methods for ids and names, but make it a possible keyword argument (get_region_from_coords(coords, as_name=True)).

Also good, as long as we have a coherent default behaviour. e.g if nothing is specified always return name.

Another thing: consistency with name and acronym, and with structure and region. I don't think we ever use the name it's usually id or acronym, so I'd avoid using name in methods and kwargs. And yeah let's decide to always call brain region regions or structures, I know I'm guilty of using both in brainrneder and it can be a bit confusing.

[vigji]

Also good, as long as we have a coherent default behaviour. e.g if nothing is specified always return name.

Absolutely - default should be the default that we use internally. I would say id.

Another thing: consistency with name and acronym, and with structure and region. I don't think we ever use the name it's usually id or acronym, so I'd avoid using name in methods and kwargs.

I agree. name is shorter and at closer mental reach, but we generally mean acronym. So either always acronym or we replace acronym->name and name->full_name.

And yeah let's decide to always call brain region regions or structures, I know I'm guilty of using both in brainrneder and it can be a bit confusing.

Fully agreed! We went some length down the structure way in the atlas generation, but if you guys like it I would move to region before it's too late, so there's a more clear anatomical connotation - and less of an IT semantic field.

[adamltyson]

I agree with this stuff generally, sorry I'm not adding much, I'm pretty busy with other work.

use either acronyms or regions ids - I would go for ids.

I would also go for ids

We went some length down the structure way in the atlas generation, but if you guys like it I would move to region

I also vote structure. In cellfinder etc., I've vaguely tried to enforce:

• structure = specific brain structure (e.g. V1)
• region = vaguer concept (e.g. a segmented injection site, or some other volume defined within the brain, usually user defined)

[FedeClaudi]

I agree. name is shorter and at closer mental reach, but we generally mean acronym. So either always acronym or we replace acronym->name and name->full_name.

I'd prefer not because most atlases, and certainly the allen atlas, use acronym/id/name so I think we should do the same.

I don't mind between structure and region, but we should enforce it asap before we build up more code

[vigji]

Ok, I guess we have a consensus.
Let's keep acronym/name and consolidate structure, I think @adamltyson point was valid here.