feat: add flatfield correction #21
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ianohara
commented
Jan 31, 2025
| channel_index = computed_params.monochrome_channels.index(channel_name) | ||
| flatfields[channel_index] = basic.flatfield | ||
| if progress_callback: | ||
| progress_callback() |
Collaborator
Author
There was a problem hiding this comment.
I think this was probably meant to be a real progress update, but we pass in the Callable[[], None] elsewhere and have a callback on our callback class specifically named for flatfield.
It may make sense to change this to flatfield progress or something, but this at least gets it working.
ianohara
commented
Jan 31, 2025
| return row_idx % 2 == 1 | ||
| case _ as unreachable: | ||
| assert_never(unreachable) | ||
| raise RuntimeError(unreachable) |
Collaborator
Author
There was a problem hiding this comment.
Looks like we can probably get this back from typing_extentions if we want to install that.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
@cjfuller implemented the actual functionality here - doing flatfield correction. It is added both as a cli option, and a checkbox in the gui.
The use of basicpy caused dependency issues, though. I was able to get a setup with just
pipworking by removing most of the constraints on the packages (I think the numpy constraint might have been the major issue?), but replicating this with uv still resulted in build issues.I also downgraded the python requirement to 3.10 since that's the default on ubuntu 22.04 lts.
Since customers seem more familiar with conda, Hongquan asked to go that route. So this now installs conda, creates a conda environment, and sets it up to work for both the cli and gui. The README should reflect this.
Tested By: Running the setup script in an ubuntu:22.04 docker container and making sure the cli worked. Also, running the same on my own computer and making sure both the cli and gui work (both with and without flatfield correction). I also made sure the tests pass, and all the dev scripts run.
Since we know the issue here were dependencies, it'd be good to have a few others test.