brainglobe / brainglobe/brainreg
registration failing when their are non-tiff files in the directory
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 150
- Forks
- 37
- Avg merge
- 3d 19h
- Merged PRs (30d)
- 5
Description
Describe the bug
Metadata in the image directory (in my case a couple of irrelevant .mat files) cause brainreg-napari to crash at the point of downsampling.
To Reproduce
Fresh installation of brainreg-napari in a clean env on linux, python 3.10. Drag directory containing all raw data images and also a couple of .mat files into napari. Choose parameters and hit run.
Expected behaviour
I would expect such an issue to crash earlier - when the data are loaded or immediately after hitting run, with a message specifically about unexpected files.
Log file
The error message I receive is:
"ValueError: Could not find a backend to open stitchedSize.mat`` with iomode ri`."
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the directory-loading and downsampling path described in the issue, then reproduce the failure with image files and a .mat file on Linux. Done means the input is rejected before downsampling with a message identifying unexpected non-TIFF files, supported by a regression test if the project has coverage for this path.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- computer-vision
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100