--compartment argument mismatch

[Glassonion]

In setting up a workflow using vanvalenlab/deepcell-applications:0.3.0 I have hit an issue with the --compartment argument.

Everything works as expected for --compartment "nuclear", however trying with --compartment "both" fails with:

/usr/local/lib/python3.6/dist-packages/tensorflow/python/keras/optimizer_v2/optimizer_v2.py:375: UserWarning: The `lr` argument is deprecated, use `learning_rate` instead.
  "The `lr` argument is deprecated, use `learning_rate` instead.")
usage: run_app.py mesmer [-h] [--output-directory OUTPUT_DIRECTORY]
                         [--output-name OUTPUT_NAME]
                         [-L {DEBUG,INFO,WARN,ERROR,CRITICAL}] [--squeeze]
                         --nuclear-image NUCLEAR_PATH
                         [--nuclear-channel NUCLEAR_CHANNEL [NUCLEAR_CHANNEL ...]]
                         [--membrane-image MEMBRANE_PATH]
                         [--membrane-channel MEMBRANE_CHANNEL [MEMBRANE_CHANNEL ...]]
                         [--image-mpp IMAGE_MPP] [--batch-size BATCH_SIZE]
                         [--compartment {nuclear,membrane,whole-cell}]
run_app.py mesmer: error: argument --compartment/-c: invalid choice: 'both' (choose from 'nuclear', 'membrane', 'whole-cell')

While --compartment "membrane" fails with:

Traceback (most recent call last):
  File "/usr/src/app/run_app.py", line 180, in <module>
    output = app.predict(image, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/mesmer.py", line 310, in predict
    postprocess_kwargs=postprocess_kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/application.py", line 448, in _predict_segmentation
    label_image = self._postprocess(output_images, **postprocess_kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/application.py", line 215, in _postprocess
    image = self.postprocessing_fn(image, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/deepcell/applications/mesmer.py", line 135, in mesmer_postprocess
    'Must be one of {}'.format(compartment, valid_compartments))
ValueError: Invalid compartment supplied: membrane. Must be one of ['whole-cell', 'nuclear', 'both']

Happy to provide more details if helpful.

[ngreenwald]

Will, we just need to change the input validation for the kwargs to match what is expected by the model.

[willgraf]

Yes, I think this is just an oversight in our argument parser?

[willgraf]

This issue is resolved in the new release (0.3.1) which should be available in the next 10-20 minutes.