Merge branch 'feature/npop3d'

* feature/npop3d:
  Add test for npop3d
  Add npop3d and teach to plot3d.neuronlist to prepare for it
  Make .plotted3d environment on startup
* part of fix for natverse/flycircuit#11

NAMESPACE

@@ -177,6 +177,7 @@ export(ngraph)
 export(nlapply)
 export(nmapply)
 export(nopen3d)
+export(npop3d)
 export(nrrd.voxdims)
 export(origin)
 export(pointsinside)
@@ -239,6 +240,7 @@ importFrom(nat.utils,makelock)
 importFrom(nat.utils,removelock)
 importFrom(rgl,par3d)
 importFrom(rgl,plot3d)
+importFrom(rgl,pop3d)
 importFrom(rgl,tmesh3d)
 importFrom(rgl,triangles3d)
 importFrom(tools,md5sum)

R/neuronlist.R

@@ -184,8 +184,13 @@ nmapply<-function(FUN, ..., MoreArgs = NULL, SIMPLIFY = FALSE, USE.NAMES = TRUE)
 #'   appropriate), the values are used to plot cell bodies. For neurons the 
 #'   values are passed to \code{plot3d.neuron} for neurons. In contrast 
 #'   \code{dotprops} objects still need special handling. There must be columns 
-#'   called \code{X,Y,Z} in the data.frame attached to \code{x}, that are then
+#'   called \code{X,Y,Z} in the data.frame attached to \code{x}, that are then 
 #'   used directly by code in \code{plot3d.neuronlist}.
+#'   
+#'   Whenever plot3d.neuronlist is called, it will add an entry to an 
+#'   environment \code{.plotted3d} in \code{nat} that stores the ids of all the
+#'   plotted shapes (neurons, cell bodies) so that they can then be removed by a
+#'   call to \code{npop3d}.
 #' @param x a neuron list or, for \code{plot3d.character}, a character vector of
 #'   neuron names. The default neuronlist used by plot3d.character can be set by
 #'   using \code{options(nat.default.neuronlist='mylist')}. See 
@@ -261,6 +266,7 @@ plot3d.neuronlist<-function(x, subset, col=NULL, colpal=rainbow, skipRedraw=200,
     if(is.logical(soma)) soma=2
     rval <- c(rval, spheres3d(df[, c("X", "Y", "Z")], radius = soma, col = cols))
   }
+  assign(".last.plot3d", rval, envir=.plotted3d)
   df$col=cols
   attr(rval,'df')=df
   invisible(rval)

R/pop3d.R

@@ -0,0 +1,19 @@
+#' Remove plotted neurons or other 3d objects
+#' 
+#' The normal usage will not specify \code{x} in which case the last neurons
+#' plotted by \code{plot3d.neuronlist} or any of its friends will be removed.
+#' @param x rgl ids of objects to remove
+#' @param slow Whether to remove neurons one by one (slowly) default: FALSE
+#' @param type Type of objects to remove see \code{pop3d}.
+#' @export
+#' @seealso \code{\link[rgl]{pop3d}}, \code{\link{plot3d.neuronlist}}
+#' @importFrom rgl pop3d
+npop3d <- function(x, slow=FALSE, type='shapes') {
+  if(missing(x)){
+    if(exists(".last.plot3d", envir=.plotted3d))
+      x <- get(".last.plot3d", envir=.plotted3d)
+    else x <- NULL
+  }
+  if(slow) invisible(sapply(x, function(x) try(pop3d(x, type=type))))
+  else try(pop3d(unlist(x), type=type))
+}

R/zzz.R

@@ -24,4 +24,7 @@
 }
 
 # will store information about formats that we can read
-.fileformats <- new.env()
+.fileformats <- new.env()
+
+# Will store stack of plotted rgl objects, ready for popping
+.plotted3d <- new.env()

man/npop3d.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
+\name{npop3d}
+\alias{npop3d}
+\title{Remove plotted neurons or other 3d objects}
+\usage{
+npop3d(x, slow = FALSE, type = "shapes")
+}
+\arguments{
+  \item{x}{rgl ids of objects to remove}
+
+  \item{slow}{Whether to remove neurons one by one (slowly)
+  default: FALSE}
+
+  \item{type}{Type of objects to remove see \code{pop3d}.}
+}
+\description{
+The normal usage will not specify \code{x} in which case
+the last neurons plotted by \code{plot3d.neuronlist} or any
+of its friends will be removed.
+}
+\seealso{
+\code{\link[rgl]{pop3d}}, \code{\link{plot3d.neuronlist}}
+}
+

man/plot3d.neuronlist.Rd

@@ -90,6 +90,12 @@ must be columns called \code{X,Y,Z} in the data.frame
 attached to \code{x}, that are then used directly by code
 in \code{plot3d.neuronlist}.
 
+Whenever plot3d.neuronlist is called, it will add an entry
+to an environment \code{.plotted3d} in \code{nat} that
+stores the ids of all the plotted shapes (neurons, cell
+bodies) so that they can then be removed by a call to
+\code{npop3d}.
+
 plot3d.character will check if
 options('nat.default.neuronlist') has been set and then use
 x as an identifier to find a neuron in that neuronlist.

tests/testthat/test-pop3d.R

@@ -0,0 +1,10 @@
+context("npop3d")
+
+test_that("pop last plotted neurons",{
+  open3d()
+  original.rgl.ids=rgl.ids()
+  plot3d(c("EBH11R", "EBH20L"), db=Cell07PNs)
+  npop3d()
+  expect_equal(rgl.ids(), original.rgl.ids)
+  rgl.close()
+})