-
Notifications
You must be signed in to change notification settings - Fork 25
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
Add MIBI tiling script #427
Conversation
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
The tests have yet to be added in, but I would appreciate an initial review of the overall structure. I'll begin tagging Erin on this PR after more progress. |
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.
Good start, see below for some initial comments
I'm researching ways to test UPDATE: the |
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, some more tweaks
Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>
Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>
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. The testing needs to be refactored.
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.
Just some thoughts on the tiling_params
structure. Agree with Noah's point on condensing/generalizing the test functions.
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.
Just minor stuff
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 amazing! My only thought would be that set_tiling_params()
is a bit long at 125 lines, mostly due to the repetitive nature of the calls to read_tiling_param()
. Breaking those calls out as their own separate functions might help condense it, but not sure if it's really worth the trouble?
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!
What is the purpose of this PR?
Begins addressing #413. We start by adding a tiling script to
ark
allowing users to generate tiled regions across fovs for a given run.How did you implement your changes
We add
example_fov_grid_generate.ipynb
, which runs the tiling process. A new repo,ark/mibi
, will contain helper functions. So far, onlytiling_utils.py
has been added to encapsulate the tiling process.Additionally, sample JSON data has been added to
data/example_dataset
.Remaining issues
Testing still needs to be addressed.