NeuriteBlast fails for FAFB neurons

[zhihaozheng]

Use appropriate credentials for FAFB login

library(catmaid)
source("../catmaid_fafb_login.R")
test_skids = c(21999,22132)
test_n=read.neurons.catmaid(test_skids, conn=conn)
r = NeuriteBlast(test_n[[1]], test_n[[2]])

The above script returns the following error:

Error in findDirectionVectorsFromParents(target, query, idxArray, ReturnAllIndices = TRUE, :
Some points do not have a parent: therefore impossible to calculate direction vector
In addition: Warning messages:
1: In .CleanupParentArray(d1[, "Parent"]) :
no points to choose in .CleanupParentArray using original value
2: In .CleanupParentArray(d2[, "Parent"]) :
no points to choose in .CleanupParentArray using original value

The error is from this function.

It seemswp=which(pa==p) will only work if the ids in d$Parent are row indices, which is not true for FAFB.

[zhihaozheng]

Of course the solution is to always convert to dotprops first (resample 1um or less, k=5). Just want to leave a note here as I ran into this again today and was at loss with what happened for ~5 mins.