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hsosik / ifcb-analysis

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How to use the Python implementation #32

Closed veot closed 3 years ago

veot commented 3 years ago

Hi, I noticed that the features_v3 branch contains a Python implementation for the feature extraction. I would like to use it to calculate biovolumes for our IFCB data, but I haven't found any information on how to go about this. A short how-to guide would be really appreciated.

veot commented 3 years ago

I have got the biovolume extraction working with the function ifcb_features.compute_features.

Because I seem to be using a newer version of numpy (1.20.1), I was getting a TypeError caused by the - operator on line 33 in morphology.py. I managed to get past it by replacing - with ^. Apparently - is depracated for boolean dtypes.

So the new line is:

bd = (binary_dilation(edges,EIGHT) & (img > T2)) ^ edges