Working cellpose-python and stardist tests

[jmetz]

NOTE: This is not ready to merge

[jmetz]

Hey @oeway - I think this looks mostly reasonable now (though let me know if you want me to remove imjoy.io from the server list).

[oeway]

Can we add some assert statements here to check the mask shape etc.? There should be a success key, and if it's false, there should be an error key to get the stack trace.

[jmetz]

Shouldn't the mask access fail if the process failed?

[jmetz]

But yeah, can check for a success key and get it's value too

[jmetz]

There is no success field... the return value is:

{
'mask': array([[0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       ...,
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0],
       [0, 0, 0, ..., 0, 0, 0]], dtype=int32), 
 '__info__': {
     'model_name': 'stardist', 
     'model_version': '1', 
     'outputs': [
         {'name': 'mask', 
           'datatype': 'INT32', 
           'shape': [349, 467], 
           'parameters': {'binary_data_size': 651932}
          }
       ]
    }
}

[jmetz]

So checking that the mask exists and contains a 2d array is probably about as good a check as we can do. Presumably it should have the same shape as the input?

NB: this is stardist not the bioengine-model-runner

[jmetz]

Just added shape tests... stardist was fine, but cellpose-python returns a stupid rolled-dimension array 🙄 :

 (1, 349, 467) != (349, 467, 3)

[jmetz]

Actually, ignore that. Upon closer paying attention, I get it 🤣 . The input is RGB, output is binary mask (and for some reason has to have the singleton dimension added).

[oeway]

Hey @oeway - I think this looks mostly reasonable now (though let me know if you want me to remove imjoy.io from the server list).

Looks good! I just added a comment. and we can keep ai.imjoy.io there.