On 14/12/2010 8:45 AM, Uwe Wolfram wrote:
Dear R-Users,
I am trying to plot an ellipsoid like function that represents some
physical threshold in its eigenvalue space. I am facing a few problems
generating a figure I need for my thesis. A small example looks as
follwos where the two contour3d plots do NOT overlay as desired so you
may try plotting the surfaces one by one to see what I mean.
====================================================================
# begin example
require(rgl)
require(misc3d)
require(MASS);
f<- function(x, y, z){
chi0=-0.6603368
eps0=0.006590395
xi0=0.01117194
(x^2 + y^2 + z^2 - chi0*(x*y + x*z + y*z))/eps0^2 + (x + y + z)/xi0
}
ff<- function(x, y, z)x + y + z
open3d()
clear3d("all")
bg3d(color="#887777")
light3d()
x<- seq(-.02,.02,len=20)
# plot ellipsoid
contour3d(f,1,x,x,x,color="#FF2222",alpha=0.5)
# plot plane
contour3d(ff,1,x,x,x,color="#FFCCCC",alpha=0.5)
# plot data points
spheres3d(c(-0.009379952, 0.007899338), c(-0.00879318, 0.00700924),
c(-0.009009740, 0.007656409),radius=0.0005,color="#CCCCFF")
# plot hydrostatic pressure line
lines3d(c(-0.012, 0.012), c(-0.012, 0.012), c(-0.012, 0.012),
col="#A8A8A8", lwd=4)
# end example
====================================================================
I have three questions regarding this problem and I hope you could help
me.
1. How can I overlay the plan plotted using contours3d(ff, ...) and
the ellipsoid plotted with contours3d(f, ...)
Use "add=TRUE" in the second call to contour3d. However, the level you
chose (i.e. 1) never occurs in the range of your x,y,z data, so you
won't see anything unless you change it.
2. Instead of using spheres3d(...) I would love to use plot3d to
obtain proper x, y and z coordinate axes. Is there a possibility
to overly the contour3d() and line3d() commands with pot3d?
Otherwise is there a possibility to plot proper coordinate axes
with tics and such as usual R plots?
Use decorate3d() to add the axes etc, or axes3d() for just axes.
3. How can I save the scene to an image? pdf(...) ... dev.off()
seems not to work on my machine. I am using Ubuntu on a 32 Bit
Laptop.
That's harder, but you can try rgl.snapshot() (for a bitmap copy in PNG
format) or rgl.postscript() (for vector graphics in
ps, eps, tex, pdf, svg, or pgf, but with incomplete rendering of some
scenes).
Duncan Murdoch
Thanks a million for your help!
Uwe
Am Montag, den 13.12.2010, 10:20 -0500 schrieb Duncan Murdoch:
> On 13/12/2010 10:13 AM, Uwe Wolfram wrote:
> >
> >
> > I am currently trying to fit a tensorial function in its principal
> > coorinate system. The function is given by:
> >
> > 1~(x1^2 + x2^2 + x3^2 - chi0*(x1*x2 + x1*x3 + x2*x3))/eps0^2 + (x1 + x2
> > + x3)/xi0
> >
> > Where eps0 = 0.0066, chi0 = -0.66 and xi0 = 0.011 are obtained from
> > experimental data using nls().I am able to plot the experimental points
> > that delivered the parameters of the function. For my thesis, however, I
> > need to overlay the fitted surface. So far I am using the following code
> > which wonderfully plots the experimental points in 3D:
> >
> > ===================================================================
> > # from demo(bivar)
> > require(rgl)
> > require(misc3d)
> > require(MASS);
> >
> > # New window
> > open3d()
> > # clear scene:
> > clear3d("all")
> > # setup env. That is, background, light and so on:
> > bg3d(color="#887777")
> > light3d()
> > # spheres at points in principal strain space
> > #spheres3d(e1,e2,e3,radius=0.00025,color="#CCCCFF")
> > # draws points alternatively
> > plot3d(e1,e2,e3, col="#CCCCFF")
> > ===================================================================
> >
> > According to the examples on http://rgl.neoscientists.org/gallery.shtml
> > I tried to overlay the point plot using surface3d. However, these were
> > only functions of type y ~f(x1, x2). I think that the surface could be
> > plotted if I could provide the gridpoints correctly. Using
> > xyz.coords(1~(x1^2 + x2^2 + x3^2 - chi0*(x1*x2 + x1*x3 + x2*x3))/eps0^2
> > + (x1 + x2 + x3)/xi0, y = NULL, z = NULL) did unfortunately not solve
> > the problem.
> >
> > Is there any function that can generate the surface for the given
> > function such as ContourPlot3D in Mathematica.
>
> See ?misc3d::contour3d
>
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