Add xform/xyzmatrix/nvertices for shapelist3d

* These changes should allow rgl::shapelist3d objects to be xformed 
  using the xform.list method.
* closes #419

NAMESPACE

@@ -18,6 +18,7 @@ S3method("xyzmatrix<-",igraph)
 S3method("xyzmatrix<-",neuron)
 S3method("xyzmatrix<-",neuronlist)
 S3method("xyzmatrix<-",shape3d)
+S3method("xyzmatrix<-",shapelist3d)
 S3method(Ops,dotprops)
 S3method(Ops,hxsurf)
 S3method(Ops,mesh3d)
@@ -105,6 +106,7 @@ S3method(nvertices,default)
 S3method(nvertices,dotprops)
 S3method(nvertices,neuron)
 S3method(nvertices,neuronlist)
+S3method(nvertices,shapelist3d)
 S3method(plot,dotprops)
 S3method(plot,neuron)
 S3method(plot,neuronlist)
@@ -172,6 +174,7 @@ S3method(xyzmatrix,igraph)
 S3method(xyzmatrix,mesh3d)
 S3method(xyzmatrix,neuron)
 S3method(xyzmatrix,neuronlist)
+S3method(xyzmatrix,shapelist3d)
 export("boundingbox<-")
 export("data.frame<-")
 export("xyzmatrix<-")

R/xform.R

@@ -279,6 +279,10 @@ xyzmatrix.neuronlist<-function(x, ...) {
   do.call(rbind, coords)
 }
 
+#' @export
+#' @rdname xyzmatrix
+xyzmatrix.shapelist3d <- xyzmatrix.neuronlist
+
 #' @export
 #' @rdname xyzmatrix
 xyzmatrix.dotprops<-function(x, ...) x$points
@@ -391,6 +395,10 @@ xyzmatrix.mesh3d<-function(x, ...){
   x
 }
 
+#' @export
+#' @rdname xyzmatrix
+`xyzmatrix<-.shapelist3d`<-`xyzmatrix<-.neuronlist`
+
 #' Find the number of vertices in an object (or each element of a neuronlist)
 #' 
 #' @param x An object with 3d vertices (e.g. neuron, surface etc)
@@ -423,6 +431,10 @@ nvertices.neuronlist <- function(x, ...) {
   sapply(x, nvertices)
 }
 
+#' @rdname nvertices
+#' @export
+nvertices.shapelist3d <- nvertices.neuronlist
+
 #' Mirror 3D object about a given axis, optionally using a warping registration
 #' 
 #' @description mirroring with a warping registration can be used to account 

tests/testthat/test-hxsurf.R

@@ -125,6 +125,12 @@ test_that("we can convert boundingbox to rgl::mesh3d",{
   expect_equal(as.mesh3d(bb), rgl::cube3d())
 })
 
+test_that("we can convert use xyzmatrix on shapelist3d object",{
+  m=as.mesh3d(MBL.surf)
+  expect_equal(xyzmatrix(shapelist3d(m, plot=F)),
+               xyzmatrix(m))
+})
+
 test_that("we can convert ashape3d to rgl::mesh3d",{
   skip_if_not_installed('alphashape3d')
   kcs20.a=alphashape3d::ashape3d(xyzmatrix(kcs20), alpha = 10)
@@ -135,7 +141,6 @@ test_that("we can convert ashape3d to rgl::mesh3d",{
   expect_true(all(pointsinside(kcs20, kcs20.a)))
 })
 
-
 test_that("we can save and re-read hxsurf object", {
   surffile <- tempfile()
   on.exit(unlink(surffile))

tests/testthat/test-xform.R

@@ -207,4 +207,5 @@ test_that("we can extract/replace coords and xform shape3d objects",{
   expect_equal(dim(xyz), c(1068L, 3L))
   # dummy transformation
   expect_equal(xform(m, function(x,...) x), m)
+  expect_equal(xform(shapelist3d(m, plot = F), function(x,...) x)[[1]], m)
 })