Skip to content
Snippets Groups Projects
Commit a1a94faa authored by Arin Wongprommoon's avatar Arin Wongprommoon
Browse files

fix!(aliby): handles alternative ref channel name when segmenting

WHY IS THIS CHANGE NEEDED?:
- ValueError raised when pipeline is run (see ref).

HOW DOES THE CHANGE SOLVE THE PROBLEM?:
(i'm still not 100% clear how the change solved the problem, but i
think this is happening...)
- BabyRunner class in aliby.baby_client assumed that the brightfield
  channel is always called 'Brightfield'; this is not true for
  experiment staffa:470 that is responsible for this bug
- i added an argument to the class so that the brightfield channel name
  string can be specified.  this extends to the classmethod as the only
  instance this class is used in the entire codebase is via this classmethod.

WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- breaks: i hard-coded the name of the brightfield channel
  'brightfield1' in pipeline.py because i couldn't think of another way to
  get it to work
- tech debt: fixing this commit exposes just how many times
  'Brightfield' is hard-coded.  this is fair because up till now, we've
  only had one name for any brightfield channel.  i suggest that the name of the
  brightfield channel be taken from the tiler parameters the user specifies.

EVIDENCE THAT COMMIT WORKS:
- run script starts segmenting without abortive errors

REFERENCES:
- issue #38
- ValueError: aliby#38 (comment 113221)
parent 88742ce3
Branches issue-038
No related tags found
No related merge requests found
Loading
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment