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

napari-aicsimage fails to read digital micrograph dm4 files #84

Open
ialxn opened this issue Oct 22, 2024 · 1 comment
Open

napari-aicsimage fails to read digital micrograph dm4 files #84

ialxn opened this issue Oct 22, 2024 · 1 comment

Comments

@ialxn
Copy link

ialxn commented Oct 22, 2024

Description

When I try to open a Gata Digital Micrograph .dm4 file I get
NoAvailableReaderError: No plugin found capable of reading OneView_600X_0092.dm4

If I just change the extension of the file to .dm3 it is read correctly (but I get the following warning)
miniforge3/envs/napari/lib/python3.12/site-packages/pydantic/_migration.py:283: UserWarning: `pydantic.error_wrappers:ValidationError` has been moved to `pydantic:ValidationError`.! SLF4J: No SLF4J providers were found. SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details.

Expected Behavior

.dm4 file should be read (maybe with the above warning). I guess napari or napari-aicsimageio selects the reader based on the file extension and .dm4 is just missing in the list of supported files.

Environment

all components installed by conda from conda-forge

python 3.12.7 hc5c86c4_0_cpython conda-forge
napari 0.5.4 hd8ed1ab_0 conda-forge
napari-aicsimageio 0.7.2 pyhd8ed1ab_1 conda-forge

@ialxn
Copy link
Author

ialxn commented Oct 29, 2024

The fix seems to be trivial. Add '*.dm4' to the known file extensions in napari_aicsimageio/napari.yaml.

filename_patterns: [ ..., '*.dm4', ... ]

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

No branches or pull requests

1 participant