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natverse / neuprintr

R client utilities for interacting with the neuPrint connectome analysis service
http://natverse.org/neuprintr
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fetching and plotting some bodyids fails in neuprintr #71

Closed lisa-marin closed 4 years ago

lisa-marin commented 4 years ago 
pvl = c(419908058, 479935033)
# can't fetch skeletons for some reason
pvl.plot = neuprint_read_neurons(pvl)
plot3d(pvl.plot, lwd = 2, col = sample(lacroix,length(pvl),replace=TRUE))

This exact same code works for other bodyids, and the bodyids listed above can be plotted in Neuprint Explorer. But in neuprintr, I get the following error message:

Error in neuprint_read_neurons(pvl) : Error: none of the given bodyids have skeletons that could be fetched

jefferis commented 4 years ago

Which version of neuprintr is Installed? We have been updating v fast. Need the github sha1 from the description field.

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On 5 Feb 2020, at 10:33, lisa-marin notifications@github.com wrote:

pvl = c(419908058, 479935033)

can't fetch skeletons for some reason

pvl.plot = neuprint_read_neurons(pvl) plot3d(pvl.plot, lwd = 2, col = sample(lacroix,length(pvl),replace=TRUE))

This exact same code works for other bodyids, and the bodyids listed above can be plotted in Neuprint Explorer. But in neuprintr, I get the following error message:

Error in neuprint_read_neurons(pvl) : Error: none of the given bodyids have skeletons that could be fetched

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lisa-marin commented 4 years ago

I just installed the latest version of neuprintr but still get the error message.

jefferis commented 4 years ago

Yes, thanks, sorry, I see that too. I think this is a slightly fiddly issue with how some neurons are healed. We (mostly Sri / Alex) basically have a solution but there are some largish changes required under the hood that I need to approve. Depending on what you need to do next, you can do:

pvl.plot = neuprint_read_neurons(pvl, heal=FALSE)

as a work around. The neurons will be in multiple pieces, but that won't stop you from plotting them etc.

jefferis commented 4 years ago

Closing as related to #32