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Command-line interface #60
jonasteuwen
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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://s3.aiforoncology.nl/ahcore/tissue_background.ckpt file_list.txt --num-gpus 2The idea is that file_list is of the form:
Additionally, we could have flags such as
--input-dirand--output-dirthat give the directory to which the paths infile_list.txtwould be relative to.What I think it requires is: a convenient script that converts such a
file_list.txtinto an in memory sqlite database, and bootstrap what we already have. Perhaps we also need something likeahcore pack-modelthat 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-inferenceandinference?Happy to hear your suggestions!
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