Incorrect segment groups imported from NML

[thorstenhater]

The points/morphology is getting imported fine, but the segment groups are not correct, e.g. the soma is going in the dendrite_group too, etc.

See NeuroML/NeuroML2#144

[noraabiakar]

I was playing with this the other day and it seemed to be working fine.

>>> import arbor
>>> tmp = arbor.neuroml("BallAndStick.cell.nml")
>>> morph = tmp.cell_morphology("BallAndStick")
>>> ns = morph.groups()
>>> print(ns)
(label_dict (region  "all" (join (join (join (join (join (join (join (join (join (join (join nil (join nil (segment 0))) (join nil (segment 1))) (join nil (segment 2))) (join nil (segment 3))) (join nil (segment 4))) (join nil (segment 5))) (join nil (segment 6))) (join nil (segment 7))) (join nil (segment 8))) (join nil (segment 9))) (join nil (segment 10)))) (region  "soma_group" (join nil (join nil (segment 0)))) (region  "dendrite_group" (join (join (join (join (join (join (join (join (join (join nil (join nil (segment 1))) (join nil (segment 2))) (join nil (segment 3))) (join nil (segment 4))) (join nil (segment 5))) (join nil (segment 6))) (join nil (segment 7))) (join nil (segment 8))) (join nil (segment 9))) (join nil (segment 10)))))

Simplified region expressions:

(label_dict 
 (region  "all" (join (segment 0) (segment 1) (segment 2) (segment 3) (segment 4) (segment 5) (segment 6) (segment 7) (segment 8) (segment 9) (segment 10))) 
 (region  "soma_group" (segment 0)) 
 (region  "dendrite_group" (join (segment 1) (segment 2) (segment 3) (segment 4) (segment 5) (segment 6) (segment 7) (segment 8) (segment 9) (segment 10))))

Edit: the following also appears correct:

>>> ns = morph.group_segments
>>> print(ns)
{'dendrite_group': [1, 2, 3, 4, 5, 6, 7, 8, 9, 10], 'soma_group': [0], 'all': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]}

[thorstenhater]

Here's the result I see when loading in the GUI:

Dendrite Group

(join (join (join (join (join (join (join (join (join (join nil (join nil (segment 1))) (join nil (segment 2))) (join nil (segment 3))) (join nil (segment 4))) (join nil (segment 5))) (join nil (segment 6))) (join nil (segment 7))) (join nil (segment 8))) (join nil (segment 9))) (join nil (segment 10)))

flattening into a list this is segments [1-10]
Soma Group

(join nil (join nil (segment 0)))

which is just [0]. So, identical to your results.

In the GUI it appears that segments [0, 1] are in the groups Soma, Dendrite, All.

[thorstenhater]

This turned out to be a feature, not a bug.

See thorstenhater/arbor-gui#31