Added torch model - Githubissues

JLrumberger commented 4 months ago

What is the purpose of this PR? Purpose is to provide an inference script/notebook that works on all platforms (linux, windows, macOS).

How did you implement your changes This PR adds the following:

the tf2torch port of the nimbus model checkpoint
class Nimbus which checks the input, loads the model, calculates the normalization dict and does whole-image or shift equivariant tile-and-stitch inference
the Unet class that implements a residual unet
the ViewerWidget class that let's the user inspect the predictions.
the updated 1_Nimbus_Predict.ipynb notebook for low-code inference.

Remaining issues

ome.tiff inference is still missing and will be added in the coming weeks.
coverage action fails, Sri will look into this.

JLrumberger commented 4 months ago

This issue explains some of the weird behavior of the github checkout action when trying to use LFS with it.

JLrumberger commented 4 months ago

@srivarra I have a hard time debugging the coveralls action. Could you look into this? It seems that .lcov files are found and uploaded but no report is generated. Thus it could be that the .lcov files are empty or that something else is preventing coveralls from returning a proper report.. Locally I generated .lcov files with pytest and transformed them to .html with coverage html and everything looks fine..

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angelolab / Nimbus-Inference

Added torch model #2