improve heal skeleton option

[jefferis]

@alexanderbates although I haven't checked in detail, the heal skeleton option looks a bit too simple to be doing the right thing. @SridharJagannathan has a new implementation that we should be able to use.

[jefferis]

See

neuprintr/R/neurons.R

Lines 183 to 198 in bf67208

	heal_skeleton <- function(x, ...){
	n = nat::as.ngraph(x)
	mstree = igraph::mst(graph = n, ...)
	healed = nat::as.neuron(mstree)
	if(healed$nTrees>1){
	fragmented = break_into_subtress(healed)
	healed = stitch_neurons(x=fragmented)
	}
	if(nat::is.neuron(x)){
	healed$connectors = x$connectors
	#healed$d = merge(healed$d, x$d)
	healed
	}else{
	healed$d
	}
	}

[SridharJagannathan]

@alexanderbates It is available here: https://github.com/natverse/nat/blob/feature/elmr_features/R/neuron.R#L1107 and will be merged to master after review by @jefferis next week.

[jefferis]

An example off a neuron that is split into 5 separate parts, 1 of which seems to be pathological. Would be good to think about giving stitch_neurons_mst an edge length threshold.

n5813054304=neuprint_read_neuron_simple(5813054304, heal = F)

[SridharJagannathan]

Hmm, just attaching the figure with the latest implementation of nat::stitch_neurons_mst where the pathological part is also connected (which needs to be fixed)

[SridharJagannathan]

I have made a new implementation in nat::stitch_neurons_mst which has a parameter thresh_el that has the edge length threshold. Only edges below this threshold will be added (currently fixed at 1000 microns). See test below (the green is the current output, overlayed on top of blue previous ouput)

[jefferis]

Just a note that we are getting close to having a fast/robust implementation of the new healing code in natverse/nat#424. There was also a separate change in as.seglist.igraph that offers significant speed-ups.

[jefferis]

Closed by #76