Command-line interface

[jonasteuwen]

Discussed in #60

^{Originally posted by jonasteuwen January 29, 2024}
Currently the inference is not straightforward to use. Since external users will most likely run the inference on the models we make available, I think we need a convenient interface.

For instance, I would propose a command like:

ahcore inference s3:https://s3.aiforoncology.nl/ahcore/tissue_background.ckpt file_list.txt --num-gpus 2

The idea is that file_list is of the form:

input_path,output_path
/input/img0.svs,/output/img0_mask.tiff
....

Additionally, we could have flags such as --input-dir and --output-dir that give the directory to which the paths in file_list.txt would be relative to.

What I think it requires is: a convenient script that converts such a file_list.txt into an in memory sqlite database, and bootstrap what we already have. Perhaps we also need something like ahcore pack-model that takes a checkpoint, and adds the configuration and other convenient metadata (version of ahcore for instance).

Probably we would also want to be able to inference on a single slide, how would we do that? Perhaps have batch-inference and inference?

Happy to hear your suggestions!