incomplete_fov_check
errors out if gold mass not specified or not named Au
#473
Labels
bug
Something isn't working
Describe the bug
In
bin_extraction.incomplete_fov_check
, the gold channel has two hard requirements as defined at https://github.com/angelolab/toffy/blob/main/src/toffy/bin_extraction.py#L105-L107:Au.tiff
.Each requirement has a problem:
Au
.Expected behavior
We should trust that users have specified their panels correctly. The current pipeline extracts every channel that is specified in the panel, so we shouldn't assume
Au
isn't specified in the panel but also was extracted.Because of the inconsistent gold naming conventions/presences across cohorts, we also need to explicitly specify
extract_intensities
as akwarg
or an explicit variable in the extraction notebook for intensity extraction. We can still default it to["Au", "chan_39"]
, but users will be able to easily modify as needed.To Reproduce
Run a cohort with gold not named
"Au"
or without gold in the panel.The text was updated successfully, but these errors were encountered: