-
Notifications
You must be signed in to change notification settings - Fork 26
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Pixie percentile saving #1020
Pixie percentile saving #1020
Conversation
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Comments about the loading process
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Agree with Alex's comments, and added just a few inconsequential naming changes.
Consulted with @alex-l-kong and removed a failing test that was resulting from the missing channel normalization code. Will get added back in #985. |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Looks good to me!
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Looks good.
If you haven't already, please read through our contributing guidelines before opening your PR
What is the purpose of this PR?
create_pixel_matrix
, not all FOVs are used to find the 99.9th percentile values #1016. Implement intermediate saving of per image 99.9th percent values.In addition, two small corrections were made to the pixie code.
channel_percentile_postnorm
argument tocreate_pixel_matrix()
, rather than hard coding 0.999.(@HPiyadasa ran into this issue when trying to pixels cluster only SMA+ pixels within a mask)
How did you implement your changes
channel_percentile_postnorm=0.999
.Remaining issues
Long term, we could probably prevent zero positive pixel images from attempting to be processed at all, but that likely requires a more in depth fix and the above solution works fine for now.