-
- Downloads
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)
Loading
Please register or sign in to comment