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plant-microct-tools / leaf-traits-microct

Functions to segment plant leaves microCT scans into distinct tissues and to extract anatomical data and other functional traits.
MIT License
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Check if testing slices are actually needed in the code #14

Open gtrancourt opened 4 years ago

gtrancourt commented 4 years ago

Testing slices are asked for in the train_model function, where they are actually not even used at all (it is not used in RandomForestClassifier).

Maybe this is a remnant from an older version of the code, like when confusion matrices were actually produced (e.g. like the functions not used anymore here and here). Let's check if they are actually used. If not, let's remove it.

Still, that does not mean we shouldn't ask users to have extra slices to test/cross-validate the predictions. Personally, I would rather suggest drawing a lot of slices for one scan, test that scan to see how many training slices should be used (incl. cross-validation on the labelled slices not used as we did in the methods paper). That way, users can focus on doing a very good test on one stack, and then using those settings on the other stacks (and not draw slices that are not really of use).

gtrancourt commented 4 years ago

I have stopped using them for the segmentations that are done in our group. Should be removed in future major update of the code. Maybe with the integration of the ubiquitousTraits branch.