R help - May 2011 - Exporting interactive 3D plots with axes and labels

Hi,

I have a question about exporting interactive 3D plots. I use the following code
to plot a contour of a trivariate normal distribution:

library(mvtnorm)
library(rgl)
library(misc3d)

n=25
x=seq(-3,3,length=n)
X=cbind(rep(x,each=n**2),rep(rep(x,each=n),n),rep(x,n**2))
p=array(dmvnorm(X,sigma=diag(3)*0.5+0.5),c(n,n,n))

contour3d(p,x,x,x,level=mean(p))
lim=c(-3,3)
decorate3d(xlim=lim,ylim=lim,zlim=lim,xlab="Variable
X",ylab="Variable Y",zlab="Variable Z")

1.      I know thanks to Luke Tierney
(www.stat.uiowa.edu/~luke/R/misc3d/misc3d-pdf/misc3d-pdf.pdf) how to export the
3D plot without the axes and labels with:

dummy=function(...){
            contour3d(p,x,x,x,level=mean(p),scale = FALSE,...)
}

conts=dummy()

saveTrianglesAsOFF <- function(scene, filename = "scene.OFF") {
            scene <- misc3d:::colorScene(scene)
            triangles <- misc3d:::canonicalizeAndMergeScene(scene,
"color", "color2",
            "alpha", "col.mesh",
            "fill", "smooth")
            ve <- misc3d:::t2ve(triangles)
            f <- file(filename, open = "w")
            on.exit(close(f))
            write("OFF", f)
            write(c(ncol(ve$vb), ncol(ve$ib), 3 * ncol(ve$ib)), f, 3)
            write(ve$vb, f, 3)
            write(rbind(3, ve$ib - 1), f, 4)
            invisible(NULL)
}

saveTrianglesAsOFF(conts,"plot.OFF")

However, I would like to have the axes and labels in the export as well. Simply
adding the decorate3d to the dummy function does not work,
nor does creating a separate dummy. (I do know how to combine multiple exports
in Meshlab).

Does anyone know how to do this in some way or the other, or is this simply not
possible?

Thanks,

Peter van Rijn

	[[alternative HTML version deleted]]

Does ?snapshot3d not do what you want? Or what do you mean by 'export' ?




remko



-------------------------------------------------
Remko Duursma
Research Lecturer

Hawkesbury Institute for the Environment
University of Western Sydney
Hawkesbury Campus, Richmond

Mobile: +61 (0)422 096908
www.remkoduursma.com



On Fri, May 13, 2011 at 6:47 AM, van Rijn, Peter <pvanrijn at ets.org>
wrote:
> Hi,
>
> I have a question about exporting interactive 3D plots. I use the following
code to plot a contour of a trivariate normal distribution:
>
> library(mvtnorm)
> library(rgl)
> library(misc3d)
>
> n=25
> x=seq(-3,3,length=n)
> X=cbind(rep(x,each=n**2),rep(rep(x,each=n),n),rep(x,n**2))
> p=array(dmvnorm(X,sigma=diag(3)*0.5+0.5),c(n,n,n))
>
> contour3d(p,x,x,x,level=mean(p))
> lim=c(-3,3)
> decorate3d(xlim=lim,ylim=lim,zlim=lim,xlab="Variable
X",ylab="Variable Y",zlab="Variable Z")
>
> 1. ? ? ?I know thanks to Luke Tierney
(www.stat.uiowa.edu/~luke/R/misc3d/misc3d-pdf/misc3d-pdf.pdf) how to export the
3D plot without the axes and labels with:
>
> dummy=function(...){
> ? ? ? ? ? ?contour3d(p,x,x,x,level=mean(p),scale = FALSE,...)
> }
>
> conts=dummy()
>
> saveTrianglesAsOFF <- function(scene, filename = "scene.OFF")
{
> ? ? ? ? ? ?scene <- misc3d:::colorScene(scene)
> ? ? ? ? ? ?triangles <- misc3d:::canonicalizeAndMergeScene(scene,
"color", "color2",
> ? ? ? ? ? ?"alpha", "col.mesh",
> ? ? ? ? ? ?"fill", "smooth")
> ? ? ? ? ? ?ve <- misc3d:::t2ve(triangles)
> ? ? ? ? ? ?f <- file(filename, open = "w")
> ? ? ? ? ? ?on.exit(close(f))
> ? ? ? ? ? ?write("OFF", f)
> ? ? ? ? ? ?write(c(ncol(ve$vb), ncol(ve$ib), 3 * ncol(ve$ib)), f, 3)
> ? ? ? ? ? ?write(ve$vb, f, 3)
> ? ? ? ? ? ?write(rbind(3, ve$ib - 1), f, 4)
> ? ? ? ? ? ?invisible(NULL)
> }
>
> saveTrianglesAsOFF(conts,"plot.OFF")
>
> However, I would like to have the axes and labels in the export as well.
Simply adding the decorate3d to the dummy function does not work,
> nor does creating a separate dummy. (I do know how to combine multiple
exports in Meshlab).
>
> Does anyone know how to do this in some way or the other, or is this simply
not possible?
>
> Thanks,
>
> Peter van Rijn
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

On 12/05/2011 4:47 PM, van Rijn, Peter wrote:
> Hi,
>
> I have a question about exporting interactive 3D plots. I use the following
code to plot a contour of a trivariate normal distribution:
>
> library(mvtnorm)
> library(rgl)
> library(misc3d)
>
> n=25
> x=seq(-3,3,length=n)
> X=cbind(rep(x,each=n**2),rep(rep(x,each=n),n),rep(x,n**2))
> p=array(dmvnorm(X,sigma=diag(3)*0.5+0.5),c(n,n,n))
>
> contour3d(p,x,x,x,level=mean(p))
> lim=c(-3,3)
> decorate3d(xlim=lim,ylim=lim,zlim=lim,xlab="Variable
X",ylab="Variable Y",zlab="Variable Z")
>
> 1.      I know thanks to Luke Tierney
(www.stat.uiowa.edu/~luke/R/misc3d/misc3d-pdf/misc3d-pdf.pdf) how to export the
3D plot without the axes and labels with:
>
> dummy=function(...){
>              contour3d(p,x,x,x,level=mean(p),scale = FALSE,...)
> }
>
> conts=dummy()
>
> saveTrianglesAsOFF<- function(scene, filename = "scene.OFF") {
>              scene<- misc3d:::colorScene(scene)
>              triangles<- misc3d:::canonicalizeAndMergeScene(scene,
"color", "color2",
>              "alpha", "col.mesh",
>              "fill", "smooth")
>              ve<- misc3d:::t2ve(triangles)
>              f<- file(filename, open = "w")
>              on.exit(close(f))
>              write("OFF", f)
>              write(c(ncol(ve$vb), ncol(ve$ib), 3 * ncol(ve$ib)), f, 3)
>              write(ve$vb, f, 3)
>              write(rbind(3, ve$ib - 1), f, 4)
>              invisible(NULL)
> }
>
> saveTrianglesAsOFF(conts,"plot.OFF")
>
> However, I would like to have the axes and labels in the export as well.
Simply adding the decorate3d to the dummy function does not work,
> nor does creating a separate dummy. (I do know how to combine multiple
exports in Meshlab).
>
> Does anyone know how to do this in some way or the other, or is this simply
not possible?
It's not currently possible, but it's on my wish list.

What you're doing is grabbing the triangles before they get sent to rgl. 
  I suppose you could try to do the same for all the axes and labels, 
but a better solution (which is what is on the wish list) is to be able 
to query an rgl scene and get back complete information (or at least 
geometric information) on every object in it.  Then you wouldn't care 
how the triangles were produced, you'd just have what you need to draw 
them again.

This isn't theoretically difficult, but it's a lot of tedious 
programming, and I just haven't needed it enough to put my nose to the 
grindstone and do it.

Duncan Murdoch