BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
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[Help] ilastik batch process step cannot find `pixel_classifier.ilp` #145

Closed Mr-Milk closed 2 years ago

Mr-Milk commented 2 years ago

After training in ilastik, I ran the following command:

steinbock classify ilastik run --ilp pixel_classifier.ilp

However, it raises an Error:

Error: Invalid value for '--ilp': File 'pixel_classifier.ilp' does not exist.

If I list the files in the directory, I can see the ilastik project file is there

> ls
ilastik_crops  ilastik_img  ilastik_probabilities  pixel_classifier.ilp
jwindhager commented 2 years ago

Hi @Mr-Milk, could you please post your steinbock alias here? Thanks

Mr-Milk commented 2 years ago

Oh! The path should be relative to the path I mount to it. I forget that this is an alias command.