core-bioimage-io-python

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Check the integrity of weights files and disable cache

2

For some reason, some weights files get corrupted after downloading, and it get saved in the cache so it always crash no matter how many times I download it. I...

oeway

Export export_resource_package as folder

1

It seems when calling `export_resource_package` it always create a zip package but it takes significant more time to load the zip package for inference compared to an extracted directory. It...

oeway

Export and load didn't work for some models

7

I am trying to maintain a installed models folder by using the following `download_model` function, then use `bioimageio.core.load_resource_description(model_path)` to load the function, but it failed for this model: "10.5281/zenodo.5911832", it...

oeway

Would it make sense to somehow link the bioimageio.spec versions with the core, namely, when running `pip install -U bioimage.core` I am kind of hope it will also upgrade the...

oeway

Widefield models not recognized by test validator

8

I have been working on the widefield models to upload them to the zoo, but there is an issue with the test validator. The models have inputs of 3 dimensions...

lmoyasans

Currently, the pytest fixtures for getting single models need to be generated by hand here: https://github.com/bioimage-io/core-bioimage-io-python/blob/main/tests/conftest.py#L177-L229. It would be nice to generate these automatically instead.

constantinpape

How to set statistics for per_dataset processing?

2

@FynnBe how do we currently deal with `per_dataset` normalization? I could not find this documented anywhere. And if I run prediction with a `per_dataset` model naively I get the following...

constantinpape

Improve documentation for the command line

3

I am trying to run model testing from a doi. In the docs it said I should do `bioimageio test-model -m ` But it said `-m` is not an option:...

oeway

> Slightly unrelated: one of the issues with the marshmallow error messages is that it does not tell you which spec it is comparing to. E.g. when you use `jsonschema`...

FynnBe

> weirdly it looks like the test input/output files do not exist? Which might also explain the error if instead of the .npy file we download some 404 response. I've...

FynnBe