Check reader for image typing

[BrianWhitneyAI]

Description

This is a potential solution to our typing discrepancy between a selected Reader and BioImage. This will make it so we do not have to add specific logic to each reader to handle unsupported filetype submission in the condition:

BioImage( ArrayLike, reader = "SOME READER THAT DOESNT SUPPORT ARRAYLIKE")

[toloudis]

As I understand it, the goal here is to basically encode the fact that only one Reader makes sense to support ArrayLike things and all the rest should be loading images from urls. I wonder if there is a more proper place in bioio-base to add that check, maybe at the base reader level. Or even have some code or flag or member variable in the ArrayLike reader that indicates that it's special. Just thinking out loud here...

I also wonder if there is a unit test you can write to test this change - do you need to make a mock reader or something like that?

[toloudis]

This function looks like it should live in plugins.py or some utility module but not in bioimage.

[BrianWhitneyAI]

resolved in 408f426

[toloudis]

annotations has different recommended ways of accessing it for python 39 and before, vs 3.10 and up. https://docs.python.org/3/howto/annotations.html

[toloudis]

Also I'm not really sure I understand how this works. Can you point to something in bioio-base or one of the readers where this "image" annotation is defined/required? It's hard to tell from just looking here (at least for me).

[BrianWhitneyAI]

The idea here was to pull the typing of the image parameter from the specified reader after it is selected and make sure they line up. An example of this would be in the ometiff reader (I think just all the readers) here where we define image as pathlike.

[BrianWhitneyAI]

annotations has different recommended ways of accessing it for python 39 and before, vs 3.10 and up. https://docs.python.org/3/howto/annotations.html

I might be missing something here. In looking at these documentations I don't believe that annotations directly apply to what we are doing. This is trying to access the typing of the init of the image whereas the examples seem to be referencing a annotation set internally by the class.

[toloudis]

annotations has different recommended ways of accessing it for python 39 and before, vs 3.10 and up. https://docs.python.org/3/howto/annotations.html

I might be missing something here. In looking at these documentations I don't believe that annotations directly apply to what we are doing. This is trying to access the typing of the init of the image whereas the examples seem to be referencing a annotation set internally by the class.

I put that link because your code uses __annotations__ (it says reader.__init__.__annotations__ right?) and the Python page I linked says:
This document is designed to encapsulate the best practices for working with annotations dicts. If you write Python code that examines __annotations__ on Python objects, we encourage you to follow the guidelines described below.

[toloudis]

Now I am wondering - I'm not sure we guarantee that all Readers have to have an __init__ constructor function that takes a named parameter called image. Is that guaranteed somewhere?

[BrianWhitneyAI]

I also wonder if there is a unit test you can write to test this change - do you need to make a mock reader or something like that?

The Idea I was thinking of is that we would include a test for each of the readers like

def test_wrongtype_param() -> None:
    with pytest.raises(exceptions.UnsupportedFileFormatError):
        test_image = np.random.rand(10, 10)
        BioImage(test_image, reader=Reader)

[toloudis]

I also wonder if there is a unit test you can write to test this change - do you need to make a mock reader or something like that?

The Idea I was thinking of is that we would include a test for each of the readers like

I was kinda wondering if you could just do one single test here in this repo (or in bioio-base) rather than add a test to every Reader, just to save the trouble

[toloudis]

LGTM! Thanks!

[kmitcham]

can be or must be?