Change index and subset file inputs to object inputs instead

[raghavmecheri]

Feature Request

Description of Problem:

You don't always have access to subset and index files saved - sometimes you want to generate them dynamically. Being able to pass in objects/arrays is more useful than passing in just filenames, especially since those filenames can just be opened and then accessed anyway.

Potential Solutions:

We may have to tweak the metadata functions that dynamically read these files, but aside from that, I think it would be a useful value-add.

@JamesBollas thoughts?

[raghavmecheri]

Closed this by including options for both in #