You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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`."
The text was updated successfully, but these errors were encountered:
Thanks for raising @stephenlenzi, we should fix this. The problem is that the brainreg plugin doesn't operate directly upon the data loaded into napari (unlike the cellfinder plugin). The data is viewed, but then the data is loaded again, in a slightly different way by brainreg (using imio). I guess we have three options with increasing elegance (and complexity for us to implement):
Warn the user if there are other files in the directory (i.e. if we think brainreg will fail)
Prevent these files from interrupting loading data with imio
Pass the data directly from napari to brainreg
If brainreg recieves a file path, it should load, downscale and save
If brainreg recieves a numpy-like obkect, it should just downscale and save
adamltyson
changed the title
[BUG]
registration failing when their are non-tiff files in the directory
Jun 27, 2023
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`."The text was updated successfully, but these errors were encountered: