Skip to content
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

Fix for nuclear speckle image display in CytoDataFrame #64

Merged
merged 11 commits into from
Aug 5, 2024

Conversation

d33bs
Copy link
Member

@d33bs d33bs commented Aug 1, 2024

Description

This PR adds fixes for bugs exhibited for nuclear speckle image data through CytoDataFrames. I found that this had to do with first a bounding box reference error (bounding box column references were static), and then second an image rendering issue (where images would not render correctly with the existing code). I made changes to these areas and added a new module for image-specific work to keep the CytoDataFrame class lean.

Along the way I found that cv2 causes an error with coverage and added a fix for this. I also added a fix to how the coverage badge renders for PyPI display (relative links don't display properly).

Thanks for any feedback you may have!

Closes #62

What kind of change(s) are included?

  • Feature (adds or updates new capabilities)
  • Bug fix (fixes an issue).
  • Enhancement (adds functionality).
  • Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

  • I have read and followed the CONTRIBUTING.md guidelines.
  • I have searched for existing content to ensure this is not a duplicate.
  • I have performed a self-review of these additions (including spelling, grammar, and related).
  • These changes pass all pre-commit checks.
  • I have added comments to my code to help provide understanding
  • I have added a test which covers the code changes found within this PR
  • I have deleted all non-relevant text in this pull request template.

@d33bs d33bs marked this pull request as ready for review August 1, 2024 23:25
@d33bs d33bs requested a review from jenna-tomkinson August 1, 2024 23:25
Copy link
Member

@jenna-tomkinson jenna-tomkinson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM! I am excited that this is so close to being ready!

media/coverage-badge.svg Outdated Show resolved Hide resolved
src/cosmicqc/frame.py Show resolved Hide resolved
src/cosmicqc/frame.py Show resolved Hide resolved
src/cosmicqc/frame.py Show resolved Hide resolved
src/cosmicqc/image.py Outdated Show resolved Hide resolved
src/cosmicqc/image.py Show resolved Hide resolved
@d33bs
Copy link
Member Author

d33bs commented Aug 5, 2024

Thanks @jenna-tomkinson for the review! Merging this in after addressing the comments.

@d33bs d33bs merged commit af7afdf into WayScience:main Aug 5, 2024
11 checks passed
@d33bs d33bs deleted the fix-for-speckle-image-display branch August 5, 2024 14:54
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

CytoDataFrame has trouble displaying nuclear speckle datasets
2 participants