Add vignette giving examples of flywire-fafb mapping

vignettes/articles/FAFB-FlyWire.Rmd

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+---
+title: "FAFB-FlyWire"
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+rgl::setupKnitr()
+havelmr=require('elmr', quietly = TRUE)
+options(nat.plotengine = 'plotly')
+```
+## Introduction
+
+This articles gives a quick overview of mapping points between FAFB14 (as used
+by the "walled garden" and [Virtual Fly Brain](https://fafb.catmaid.virtualflybrain.org/) and [FlyWire](https://flywire.ai).
+
+```{r setup}
+library(fafbseg)
+```
+
+### Basic point mapping
+Some known points 
+```{r}
+# identified location in FAFB14
+p.fafb.nm <- cbind(477042, 284535, 90680)
+p.fafb.raw <- p.fafb.nm/c(4,4,40)
+# corresponding location in FlyWire
+p.flywire.raw <- cbind(118865, 71338, 2267)
+p.flywire.nm <- p.flywire.raw * c(4,4,40)
+```
+
+Compare displacements (in nm) for forward or inverse mapping
+```{r}
+# check displacement
+flywire2fafb(p.flywire.nm)-p.fafb.nm
+
+# check what happens when you apply the inverse
+fafb2flywire(p.fafb.nm)-p.flywire.nm
+```
+
+
+A sample neuron. First map the points
+```{r}
+data("AV4b1", package='catmaid')
+before=xyzmatrix(AV4b1)
+after=fafb2flywire(before)
+```
+
+Then some stats and a quick histogram
+```{r}
+d=sqrt(rowSums((before-after)^2))
+summary(d)
+```
+
+```{r}
+hist(d, br=20, main='Displacement /µm')
+```
+
+```{r}
+sample_points_in_surf <- function(x, n){
+  x=as.mesh3d(x)
+  bb=boundingbox(x)
+  mm=mapply(runif, min=bb[1,], max=bb[2,], n = n)
+  colnames(mm)=c("X","Y","Z")
+  data.frame(mm, inside=pointsinside(mm,x))
+}
+
+```
+
+```{r, eval=havelmr, cache=T}
+set.seed(42)
+sxyz=sample_points_in_surf(FAFB14.surf,25000)
+sxyz.in=subset(sxyz, inside)
+sxyz.fw=fafb2flywire(xyzmatrix(sxyz.in))
+deltas=sxyz.fw-sxyz.in
+delta=rowSums(deltas[,c("X","Y")])
+```
+
+```{r, webgl=T, eval=havelmr}
+jet.colors<-colorRampPalette(c('navy','cyan','yellow','red'))
+nclear3d();
+spheres3d(xyzmatrix(sxyz.in), col=jet.colors(10)[cut(delta, breaks = 10)], rad=2000)
+```
+
+### Round trip error
+Let's send those points back again
+```{r, cache=T}
+sxyz.fafb2=flywire2fafb(sxyz.fw)
+```
+
+```{r}
+deltas=sxyz.fafb2-xyzmatrix(sxyz.in)
+delta=rowSums(deltas[,c("X","Y")])
+hist(delta, main = "Round Trip Error", xlab='delta /nm')
+```
+
+## Mapping anything
+
+To map complex objects, use `xform_brain()`
+
+```{r, cache=T}
+AV4b1.fw=xform_brain(AV4b1, sample='FAFB14', reference = 'FlyWire')
+```
+
+```{r}
+# find the main branch point of a neuron, a good place to point to
+mainbranch <- function(x, ...) {
+  if(is.neuronlist(x)) 
+    return(nlapply(x, mainbranch, ...))
+  
+  sx=nat::simplify_neuron(x, ...)
+  xyzmatrix(sx)[sx$BranchPoints,]
+}
+```
+
+```{r}
+choose_segmentation("flywire")
+open_fafb_ngl(mainbranch(AV4b1.fw), coords.only = TRUE)
+```
+
+![catmaid](catmaid-av4.png){width=400px}
+![catmaid](flywire-av4.png){width=800px}
+
+Load the flywire mesh 
+
+```{r, cache=TRUE, message=FALSE}
+av4.fwm=read_cloudvolume_meshes('720575940618054533')
+```
+
+
+And plot with the CATMAID skeleton
+
+```{r}
+nclear3d()
+plot3d(AV4b1.fw, col='red', lwd=2)
+shade3d(av4.fwm[[1]], col='grey', alpha=.2)
+```
+
+It's obvious that both are only partially traced