Merge branch 'master' into so_fix

DESCRIPTION

@@ -6,7 +6,8 @@ Authors@R: c(
     person("Gregory","Jefferis", email="jefferis@gmail.com", 
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0587-9355")),
     person("James", "Manton", role = c("aut"), comment = c(ORCID = "0000-0001-9260-3156")),
-    person("Sridhar", "Jagannathan", role = c("aut"), comment = c(ORCID = "0000-0002-2078-1145"))
+    person("Sridhar", "Jagannathan", role = c("aut"), comment = c(ORCID = "0000-0002-2078-1145")),
+    person("Dominik", "Krzeminski", role = c("ctb"), comment = c(ORCID = "0000-0003-4568-0583"))
     )
 URL: https://github.com/natverse/nat, https://natverse.github.io
 BugReports: https://github.com/natverse/nat/issues

NAMESPACE

@@ -19,6 +19,7 @@ S3method("xyzmatrix<-",default)
 S3method("xyzmatrix<-",dotprops)
 S3method("xyzmatrix<-",hxsurf)
 S3method("xyzmatrix<-",igraph)
+S3method("xyzmatrix<-",mesh3d)
 S3method("xyzmatrix<-",neuron)
 S3method("xyzmatrix<-",neuronlist)
 S3method("xyzmatrix<-",shape3d)
@@ -184,6 +185,7 @@ S3method(xform,data.frame)
 S3method(xform,default)
 S3method(xform,dotprops)
 S3method(xform,list)
+S3method(xform,mesh3d)
 S3method(xform,neuron)
 S3method(xform,neuronlist)
 S3method(xform,shape3d)

NEWS.md

@@ -8,6 +8,9 @@ Some new features and bug fixes. Thanks to @PostPreAndCleft and @artxz for repor
 * Fix bug `pan3d()` not found (#447)
 * Added support for multi material binary Amira surface files while fixing
   "Bad triangle numbers" error in `read.hxsurf()` (#445)
+* Add `xform()` and `xyzmatrix<-()` methods for `mesh3d` objects
+* Don't clean `mesh3d` objects read from ply files by default
+* `summary.neuron` now prints number of subtrees (#462, @dokato)
 
 # nat 1.10.2
 

R/dotprops.R

@@ -155,7 +155,7 @@ dotprops.neuronlist<-function(x, ..., OmitFailures=NA) {
 #' @param resample When finite, a new length to which all segmented edges will
 #'   be resampled. See \code{\link{resample.neuron}}.
 #' @param topo flag that says whether or not to add topological features
-#' (inverted Strahler's Order and distance from soma)
+#' (reversed Strahler Order and distance from soma)
 #' @rdname dotprops
 dotprops.neuron<-function(x, Labels=NULL, resample=NA, topo=FALSE, ...) {
   if(is.finite(resample)) x=resample(x, stepsize = resample)
@@ -212,7 +212,7 @@ get_distance_to_soma <- function(n) {
 #'   behaviour for different classes of input object, \code{TRUE} always uses 
 #'   labels when an incoming object has them and \code{FALSE} never uses labels.
 #' @param na.rm Whether to remove \code{NA} points (default FALSE)
-#' @param topo_features topological features of each dotprop
+#' @param topo_features topological features of each dotprops
 #' @importFrom nabor knn
 #' @references The dotprops format is essentially identical to that developed 
 #'   in:

R/neuron-mesh.R

@@ -1,12 +1,15 @@
 # internal function
 # read a mesh representing a neuron and return a mesh3d object
-read.neuron.mesh <- function(x, ...) {
+read.neuron.mesh <- function(x, updateNormals=FALSE, clean=FALSE, ...) {
   ext=tools::file_ext(x)
 
   if(ext=="ply") {
     if(!requireNamespace('Rvcg', quietly = TRUE))
       stop("Please install suggested library Rvcg to read .ply files!")
-    Rvcg::vcgPlyRead(x, updateNormals=F, ...)
+    m=Rvcg::vcgPlyRead(x, updateNormals=updateNormals, clean=clean, ...)
+    if(!inherits(m, 'shape3d'))
+      class(m)=union(class(m), 'shape3d')
+    m
   } else if(ext=="obj") {
     if(!requireNamespace('readobj', quietly = TRUE))
       stop("Please install suggested library readobj to read .obj files!")

R/summary.R

@@ -39,6 +39,8 @@ summary.neuronlist<-function(object, ..., include.attached.dataframe=FALSE) {
 #'   
 #'   \item{cable.length}
 #'   
+#'   \item{nTrees}
+#'   
 #'   }
 #' @export
 #' @examples 
@@ -50,7 +52,8 @@ summary.neuron<-function(object, ...) {
              segments=object$NumSegs,
              branchpoints=length(object$BranchPoints),
              endpoints=length(object$EndPoints),
-             cable.length=total_cable(object))
+             cable.length=total_cable(object),
+             nTrees=ifelse("nTrees" %in% names(object), object$nTrees, 1))
 }
 
 #' @export

R/xform.R

@@ -112,6 +112,10 @@ xform.list<-function(x, reg, FallBackToAffine=TRUE, na.action='error', ...){
 #' @rdname xform
 xform.shape3d<-xform.list
 
+#' @export
+#' @rdname xform
+xform.mesh3d<-xform.list
+
 #' @export
 #' @rdname xform
 xform.neuron<-xform.list
@@ -512,6 +516,11 @@ xyzmatrix.mesh3d<-function(x, ...){
   x
 }
 
+#' @export
+#' @rdname xyzmatrix
+`xyzmatrix<-.mesh3d`<-`xyzmatrix<-.shape3d`
+
+
 #' @export
 #' @rdname xyzmatrix
 `xyzmatrix<-.neuronlist`<-function(x, value){

tests/testthat/test-summary.R

@@ -2,7 +2,7 @@ context("summary")
 
 test_that("summary.neuronlist behaves", {
   expect_is(s <- summary(Cell07PNs), 'data.frame')
-  expect_equal_to_reference(s, file = 'testdata/summary_cell07pns.rda', tolerance=1e-3)
+  expect_equal_to_reference(s, file = 'testdata/summary_cell07pns.rds', tolerance=1e-3)
   expect_is(summary(kcs20, veclength=1.2), 'data.frame')
 })