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

Detect VisiumHD full-res image when path is relative #230

Open
wants to merge 1 commit into
base: main
Choose a base branch
from

Conversation

quentinblampey
Copy link
Contributor

There is a minor bug in the Visium HD reader. When we provide a relative path to the data, e.g. "data/Visium_HD_Mouse_Small_Intestine", then it will search for the microscopy image inside "data/Visium_HD_Mouse_Small_Intestine/data/Visium_HD_Mouse_Small_Intestine/microscope_image".

This is because it was using path / fullres_image_file instead of simply fullres_image_file.

I also did some minor updates to use pathlib everywhere instead of a combination of pathlib and os (it makes the code more readable I think).

@codecov-commenter
Copy link

codecov-commenter commented Oct 31, 2024

Codecov Report

Attention: Patch coverage is 0% with 3 lines in your changes missing coverage. Please review.

Project coverage is 45.50%. Comparing base (cff4896) to head (35232d0).
Report is 5 commits behind head on main.

Files with missing lines Patch % Lines
src/spatialdata_io/readers/visium_hd.py 0.00% 3 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #230      +/-   ##
==========================================
- Coverage   45.50%   45.50%   -0.01%     
==========================================
  Files          22       22              
  Lines        2149     2147       -2     
==========================================
- Hits          978      977       -1     
+ Misses       1171     1170       -1     
Files with missing lines Coverage Δ
src/spatialdata_io/readers/visium_hd.py 18.29% <0.00%> (-0.39%) ⬇️

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.

2 participants