AllenInstitute/AllenSDK

Violation of SWC spec in at least three files

patrick-nicodemus opened this issue · 1 comments

I apologize if this is not the appropriate place for this comment.
The SWC spec here requires that "Parent samples must be defined before they are being referred to."
https://neuroinformatics.nl/swcPlus/
The SWC spec described here requires that "Parent samples should appear before any child samples"
http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html

In these three SWC files:
https://celltypes.brain-map.org/experiment/morphology/569965244
https://celltypes.brain-map.org/experiment/morphology/580007431
https://celltypes.brain-map.org/experiment/morphology/590558808
this requirement is violated.
The first one, if you open the associated SWC file in a text editor, reads

#name
#comment
##n,type,x,y,z,radius,parent
1 1 389.2185 749.32 19.6823 6.9945 -1
2 2 397.8924 754.8432 20.3437 0.1144 3
3 2 396.7712 754.7815 20.1214 0.1144 4
4 2 395.6867 754.4794 19.9651 0.1151 5

The last number in each line should be strictly less than the first number in each line. In other words, the graph should be topologically sorted.

@patrick-nicodemus could you please post that instead to https://community.brain-map.org/ ? The current team that maintains AllenSDK is not familiar with this. If someone replies that it's relevant to AllenSDK then we can reopen this issue.