[R] Question about contour3d and writeWebGL: rgl and misc3d package

[Duncan Murdoch]

On 12-11-17 1:51 PM, John Muschelli wrote:
> That works!  Thanks for the help, but I can't seem to figure out why
> this happens with even one contour in the example below:
> Disclaimer: using MNI template from FSL
> (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases).
>
> Firefox still has array initialiser too large for this one contour, but
> Safari and Chrome both will render it, but again it comes out half of a
> brain and the vertices are connected across the brain and not a surface.
>
> The code is the same as with the example from AnalyzeFMRI, but a
> different dimension for the array and a different level (Also attached).

There's a thread from last year here:

https://www.khronos.org/webgl/public-mailing-list/archives/1102/msg00093.html

that says that WebGL is limited to 65535 vertices in any object.  I 
assume that limit is still in effect, and your scenes probably have too 
many vertices.

The writeWebGL function doesn't do any checks for things like this. 
I'll think about having it split up objects as required, but in the 
meantime, you'll need to do it yourself.

Duncan Murdoch

>
> template<- f.read.nifti.volume("MNI152_T1_2mm_brain.nii")
>
> template<-template[,,,1]
>
>
> contour3d(template,x=1:dim(template)[1],y=1:dim(template)[2],z=1:dim(template)[3],level=c(1000),alpha
> =c(0.2),color =c("white"))
>
> browseURL(paste("file://",writeWebGL(dir=file.path(tempdir(),"webGL"),
>
>            width=500), sep=""))
>
>
>
>
> On Fri, Nov 16, 2012 at 8:37 PM, Duncan Murdoch
> <murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>> wrote:
>
>     On 12-11-16 7:09 PM, John Muschelli wrote:
>
>         The contour its just half a brain and the vertices are not
>         surfaces and
>         are filled in
>
>
>     Sounds like a bug in the browser.  When I try it in Firefox 16.0.2
>     it doesn't display properly; the error log (found via Tools | Web
>     developer | Error console has several errors in it, the first of
>     which is:
>
>     Error: array initialiser too large
>
>     That's clearly a limitation of the browser.  You might be able to
>     work around it by plotting one layer at a time; writeWebGL will
>     write each rgl object in separate arrays of data.  If the layers are
>     separate, the browser might be able to handle them.  I just tried
>     this, and it works on my system, using this code:
>
>
>     contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000),
>       alpha = c(0.2), color = c("white"))
>
>       contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(8000),
>       alpha = c(0.5), color = c("red"), add=TRUE)
>
>       contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(10000),
>       alpha = c(1), color = c("green"), add=TRUE)
>
>     followed by the browseURL call you already had.
>
>     Duncan Murdoch
>
>
>
>         This was sent from a mobile phone so please excuse any
>         misspellings or
>         typos.
>
>         On Nov 16, 2012 6:55 PM, "Duncan Murdoch"
>         <murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>
>         <mailto:murdoch.duncan at gmail.__com
>         <mailto:murdoch.duncan at gmail.com>>> wrote:
>
>              On 12-11-16 5:59 PM, John Muschelli wrote:
>
>                  I saw that in rgl:::writeWebGL that "Polygons will only be
>                  rendered as
>                  filled; there is no support in WebGL for wireframe or point
>                  rendering.".  I
>                  found that you can easily use contour3d to make
>         reproducible
>                  contour web
>                  figures, such as (taken from contour3d help)
>
>                      library(AnalyzeFMRI)
>
>                      a <-
>         f.read.analyze.volume(system.____file("example.img", package=
>
>                  "AnalyzeFMRI"))
>
>                      a <- a[,,,1]
>
>                      contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000),
>
>                                alpha = c(0.2), color = c("white"))
>
>                  browseURL(paste("file://",
>         writeWebGL(dir=file.path(____tempdir(),
>
>                  "webGL"),
>
>                              width=500), sep=""))
>
>                  But I found problems with multiple levels, such as
>
>                      contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000,
>         8000, 10000),
>
>                                alpha = c(0.2, 0.5, 1), color =
>         c("white", "red",
>                  "green"))
>
>
>                  browseURL(paste("file://",
>         writeWebGL(dir=file.path(____tempdir(),
>
>                  "webGL"),
>
>                              width=500), sep=""))
>
>
>                  Does anyone know why this happens, or a way to fix it
>         (maybe
>                  using separate
>                  = TRUE for contour3d)?
>
>
>              Why what happens?
>
>              Duncan Murdoch
>
>
>