Input data format

[smguo]

Dynamorph currently assumes "XX-SITE_#" for input file names (with XX being the well name A1, B1, ...) for all the CLI. This is not compatible with data that not are acquired with mManager HCS plugin, where the file structure is usually "XXX/img_p###.npy".

We can reconcile this difference or have different data parsers for HCS and non-HCS data. I think it's cleaner to have images from different wells/conditions organized in different folders rather than embedding the well names/conditions in the file names and assuming specific name format. But both solutions would work.

Let me know your thoughts @miaecle @bryantChhun @mattersoflight .