Add xyzmatrix2list xyzmatrix<-.list

* should allow handling of arrow list of vectors
* includes tests

NAMESPACE

@@ -19,6 +19,7 @@ S3method("xyzmatrix<-",default)
 S3method("xyzmatrix<-",dotprops)
 S3method("xyzmatrix<-",hxsurf)
 S3method("xyzmatrix<-",igraph)
+S3method("xyzmatrix<-",list)
 S3method("xyzmatrix<-",mesh3d)
 S3method("xyzmatrix<-",neuron)
 S3method("xyzmatrix<-",neuronlist)
@@ -375,6 +376,7 @@ export(xform)
 export(xformimage)
 export(xformpoints)
 export(xyzmatrix)
+export(xyzmatrix2list)
 export(xyzmatrix2str)
 export(xyzpos)
 import(grDevices)

R/xyzmatrix.R

@@ -186,6 +186,13 @@ xyzmatrix.mesh3d<-function(x, ...){
 #' ))
 `xyzmatrix<-`<-function(x, value) UseMethod("xyzmatrix<-")
 
+#' @export
+`xyzmatrix<-.list`<-function(x, value) {
+  if(!isTRUE(nrow(value)==length(x)))
+    stop("target list and new value have incompatible sizes")
+  xyzmatrix2list(value)
+}
+
 #' @export
 `xyzmatrix<-.default`<-function(x, value){
   # count number of elements in matrices/data.frames and vectors
@@ -274,6 +281,20 @@ xyzmatrix2str <- function(x, format="%g,%g,%g", sep=NULL) {
   sprintf(format, xyz[,1], xyz[,2], xyz[,3])
 }
 
+
+#' @rdname xyzmatrix
+#' @export
+#' @description  \code{xyzmatrix2list} will convert the Nx3 matrix of XYZ
+#'   locations associated with an object to a list of length N with each element
+#'   a vector of length 3.
+#' @examples
+#' xyzmatrix2list(kcs20[[1]])[1:2]
+xyzmatrix2list <- function(x) {
+  xyz <- unname(xyzmatrix(x))
+  ll=lapply(1:nrow(xyz), function(i) xyz[i,])
+  ll
+}
+
 #' @export
 #' @rdname xyzmatrix
 `xyzmatrix<-.neuron`<-function(x, value){

tests/testthat/test-xyzmatrix.R

@@ -112,6 +112,10 @@ test_that("can extract xyz coords from a matrix and other objects",{
     baseline,
     tolerance = 1e-6
   )
+
+  xyzmatrix(arrowdf$pt_position) <- xyzmatrix(arrowdf$pt_position)+1
+  expect_equal(xyzmatrix(arrowdf$pt_position), 
+               baseline+1, tolerance = 1e-6)
 })
 
 test_that("can replace xyz coords of a matrix",{
@@ -193,6 +197,17 @@ test_that("can replace xyz coords of a data.frame",{
 })
 
 
+test_that("can get/replace xyz coords in a list",{
+  xyzm <- xyzmatrix(kcs20)
+  df <- data.frame(a=1:sum(nvertices(kcs20)))
+  expect_true(is.list(xyzml <- xyzmatrix2list(kcs20)))
+  expect_true(all(lengths(xyzml)==3L))
+  df$pos=xyzmatrix2list(kcs20)
+  xyzmatrix(df$pos)=xyzmatrix(df$pos)+1
+  expect_equal(xyzmatrix(df$pos), xyzmatrix(kcs20+1))
+})
+
+
 test_that("can extract xyz coords from a neuronlist",{
   xyz12=rbind(xyzmatrix(kcs20[[1]]),xyzmatrix(kcs20[[2]]))
   expect_is(xyzmatrix(kcs20[1:2]),'matrix')