ideas for refactoring: image_parser module is too large

[bryantChhun]

The extract.image_parser module has become a catch-all of functions. Many of these can be moved out.

I'll start by doing the following across two PRs:

1. copying functions to new modules in appropriate locations
2. changing import statements to the new modules/locations
3. finally, remove the old functions from the old modules (maybe a 3rd PR?)

[mattersoflight]

I suggest creating one PR with refactor to which multiple individuals contribute and initiate one or two PRs. Our goal should be to describe dataflow with names of the modules/functions.

For example,

Load images and metadata, write output:

io.load_scienion(path, metadata)
io.load_octopi(path, metadata)
io.save_OD()
io.save_intensities()
io.save_background()

Image->OD per well:

analyze.segment_well
analyze.compute_background
analyze.find_array_spots
analyze.compute_OD

debug plots:
debug.plot_overlay
debug.plot_icp

OD->calls across wells:
measure.standard_curve
measure.plot_OD(antigen,serum)
measure.antibody_concentration

The last module (measure ) needs to be defined.

[bryantChhun]

I suggest creating one PR with refactor to which multiple individuals contribute and initiate one or two PRs. Our goal should be to describe dataflow with names of the modules/functions.

One difficulty with this approach is that there can not be any permission, PR, or other check that someone pushes changes we all agree upon. Contributors to this branch will simply "push to remote". And all other contributors will have to frequently "pull from origin" and resolve conflicts to make sure we are synched with new pushes.

It is possible to do PR to this branch. I think we each can have a repo fork and submit a PR across forks/branches.