Skip to content

Make thumbnail for lamella evaluation images - #898

Merged
tieneupin merged 6 commits into
mainfrom
make-thumbnail-image
Sep 23, 2026
Merged

tieneupin merged 6 commits into
mainfrom
make-thumbnail-image

Conversation

@tieneupin

@tieneupin tieneupin commented Sep 23, 2026 •

Copy link
Copy Markdown
Contributor

Another scoped PR to extend the lamella image registration workflow. Adds the logic needed to save a thumbnail image of the incoming lamella image to the path "{visit_dir}/processed/grid_{slot_number}/lamella_evaluation_images/lamella_{lamella_number}_{timestamp}_{step_name}.png".

The main run test for this workflow has also been overhauled so that it is run using the test database session we have set up, to verify that database inserts are correct. This will be heavily made use of as the workflow is further extended and more database inserts and calls are added.

Additionally, minor optimisations were made to the atlas registration workflow to improve readability and memory management when opening images.

@codecov

codecov Bot commented Sep 23, 2026 •

Copy link
Copy Markdown

Codecov Report

❌ Patch coverage is 82.60870% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.11%. Comparing base (d28bf70) to head (84e30bd).

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #898      +/-   ##
==========================================
+ Coverage   55.08%   55.11%   +0.03%     
==========================================
  Files         103      103              
  Lines       11532    11550      +18     
  Branches     1530     1531       +1     
==========================================
+ Hits         6352     6366      +14     
- Misses       4838     4841       +3     
- Partials      342      343       +1     
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@tieneupin tieneupin self-assigned this Sep 23, 2026
@tieneupin tieneupin added enhancement New feature or request server Relates to the server component fib Part of the FIB pipeline extension labels Sep 23, 2026
@tieneupin
tieneupin marked this pull request as ready for review September 23, 2026 15:29

@stephen-riggs stephen-riggs left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

Looks fine. It relies heavily on the file naming being in the expected form, but I think that should be ok.

@tieneupin
tieneupin merged commit 3acb9f5 into main Sep 23, 2026
26 checks passed
@tieneupin
tieneupin deleted the make-thumbnail-image branch September 23, 2026 16:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

enhancement New feature or request fib Part of the FIB pipeline extension server Relates to the server component

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants