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Add the bioimageio resource description to deserialized stardist model #187

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Mar 22, 2022
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Add the bioimageio resource description to deserialized stardist model #187

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Add the bioimageio resource description to deserialized stardist model
constantinpape Mar 18, 2022
8608aec
Update import_bioimageio to save complete bioimageio model to output …
constantinpape Mar 22, 2022
0e531ea
Change import_bioimageio
uschmidt83 Mar 22, 2022
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9 changes: 9 additions & 0 deletions stardist/bioimageio_utils.py
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Expand Up @@ -453,4 +453,13 @@ def import_bioimageio(source, outpath):

model_class = (StarDist2D if config['n_dim'] == 2 else StarDist3D)
model = model_class(None, outpath.name, basedir=str(outpath.parent))

# update the location of the stardist specific files, since they are the ones being used by the model
biomodel.config['stardist']['config'] = outpath / 'config.json'
biomodel.config['stardist']['thresholds'] = outpath / 'thresholds.json'
biomodel.config['stardist']['weights'] = outpath / weights
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Why is this helpful?

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E.g. to have the correct weight path that the stardist model is using, for example in the case where weights are updated.

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Sorry, I don't get it. If you want the preserve the config, thresholds, and weights at the time when the bioimage.io model was imported, then why should biomodel.config['stardist']['config'] and biomodel.config['stardist']['thresholds'] be overwritten?

# add the resource description as an attribute to the model,
# so that additional information stored in there does not get lost
model.bioimageio_resource_description = biomodel
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return model