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[ENH] topoDotprops modified #502

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[ENH] topoDotprops modified #502

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26 changes: 23 additions & 3 deletions R/dotprops.R
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,11 @@ dotprops.neuron<-function(x, Labels=NULL, resample=NA, topo=FALSE, ...) {
if(is.null(Labels) || isTRUE(Labels)) Labels=x$d$Label
else if(is.logical(labels) && labels==FALSE) Labels=NULL
topo_features <- NULL
if (isTRUE(topo)) topo_features <- get_topo_features(x)
if (isTRUE(topo)) {
topo_features <- get_topo_features(x)
topo_features$Parent <- x$d$Parent
topo_features$PointNo <- x$d$PointNo
}
dotprops(xyzmatrix(x), Labels=Labels, topo_features=topo_features, ...)
}

Expand Down Expand Up @@ -261,17 +265,33 @@ dotprops.default<-function(x, k=NULL, Labels=NULL, na.rm=FALSE, topo_features=NU
vect[i,]=v1d1$vectors[,1]
}
rlist=list(points=x,alpha=alpha,vect=vect)

rlist$labels=Labels

if (!is.null(topo_features)) {
# orient vectors so they look at their parent
vect_orientations <- rep(TRUE, npoints)
for (i in 1:npoints) {
par_id = topo_features$Parent[[i]]
if (par_id == -1) next
pnt_idx = which(topo_features$PointNo == par_id)
vect_orientations[[i]] <- is_pointing_towards(x[pnt_idx,], x[i,], vect[i])
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this is direction in Euclidean sense not geodesic (across the graph). Can you help me understand why that is @dokato?

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I just figured that it's faster to compute with respect to an arbitrary point (soma in this case). Otherwise, I'd need to iterate point by point to change the orientation. I guess, as long as it's consisted it shouldn't matter too much, unless you can think of some counterexample?

}
vect[!vect_orientations,] <- -vect[!vect_orientations,]
rlist$vect = vect
topo_features$Parent <- NULL
topo_features$PointNo <- NULL
rlist$topo <- topo_features
}

attr(rlist,'k')=k
return(as.dotprops(rlist))
}

is_pointing_towards <- function(soma_position, point_pos, vects) {
to_point <- soma_position - point_pos
dotprod(to_point, vects) > 0
}

# internal function to convert a dotprops object to SWC
# representation.
dotprops2swc<-function(x, label=0L, veclength=1, radius=0) {
Expand Down