Re: [R] Plotting a cloud/fog of variable density in rgl
Thanks for both the replies. I think you can come closest to what you want within rgl by using sprites rather than rendering transparent spheres. See examples(sprites3d). Sprites helps a lot indeed. With enough transparency I am close to what I want. If you only have 2 things with simple properties, namely point emitters as your organisms and a uniform concsntration of transparent scatters ( the fog) you can probably derive geometrical optics expressions for the ray trace results and just integrate those over your source distribution. This should be reasonably easy in R. I haven't been to siggraph since 1983 so can't help much but you can probably find analyitcal solutions for fog on google and just sum up your source distribution. I guess you could even do some wave optics etc as presumably the fog could be done as a function of wavelength just as easily. In any case, if you only have two basic things with simple disto should be reasonably easy to do in R with your own code. I am afraid this is a bit too advanced for me. I know next to nothing regarding digital 3D imaging and, even if I could compute this, I am not sure how I would plot the result. My goal is really to add this to my R-plotting arsenal and use it in routine, not to develop something very specific for this particular application. But thank you for taking the time to reply, maybe I'll come back to this when I know more. JiHO --- http://maururu.net __ R-help@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.
[R] Plotting a cloud/fog of variable density in rgl
Hi everyone, I want to plot a 3D interpolation of the concentration of aquatic organisms. My goal would be to have the result represented as clouds with a density proportional to the abundance of organisms, so that I could fly (well, swim actually ;) ) through the scene and see the patches here and there. Basically, I want to do something like this: http://www.youtube.com/watch?v=27mo_Y-aU-c but simpler and with only clouds. I though about doing it this way: 1- interpolate to a fine grid 2- plot points at each grid intersection of transparency inversely proportional to abundance 3- blur/fog a bit each point to create the general impression of a cloud So far I am stuck on 3 but maybe there is a better overall solution. Here is some code that reads the result of the interpolation on a coarse grid and plots it: # read a set of gridded data points in 3D d = read.table(http://dl.dropbox.com/u/1047321/R/test3Ddata.txt;, header=T) # plot library(rgl) spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05) And here is a version that actually performs the interpolation a random set of points in 3D through kriging in case you want to try with increase precision. # create a set of random data points in 3D n = 50 data3D = data.frame(x = runif(n), y = runif(n), z = runif(n), v = rnorm(n)) # do 3d interpolation via kriging library(gstat) coordinates(data3D) = ~x+y+z range1D = seq(from = 0, to = 1, length = 10) grid3D = expand.grid(x = range1D, y = range1D, z = range1D) gridded(grid3D) = ~x+y+z res3D = krige(formula = v ~ 1, data3D, grid3D, model = vgm(1, Exp, .2)) # convert the result to a data.frame d = as.data.frame(res3D) # compute transparency (proportional to the interpolated value) maxD = max(d$var1.pred) minD = min(d$var1.pred) alpha = (d$var1.pred - minD)/(maxD - minD) # reduce maximum alpha (all points are semi-transparent) alpha = alpha/5 # plot library(rgl) spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05) I saw the fog effect but it seems to add a fog in the scene to increase depth. What I want is my scene to actually look like a fog. Thanks in advance for any help. Sincerely, JiHO --- http://maururu.net __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting a cloud/fog of variable density in rgl
On 22/11/2010 12:51 PM, JiHO wrote: Hi everyone, I want to plot a 3D interpolation of the concentration of aquatic organisms. My goal would be to have the result represented as clouds with a density proportional to the abundance of organisms, so that I could fly (well, swim actually ;) ) through the scene and see the patches here and there. Basically, I want to do something like this: http://www.youtube.com/watch?v=27mo_Y-aU-c but simpler and with only clouds. rgl doesn't make everything in OpenGL available. I'm not sure exactly how those clouds were done, but it wouldn't really be easy to do them in rgl. I think you can come closest to what you want within rgl by using sprites rather than rendering transparent spheres. See examples(sprites3d). Duncan Murdoch I though about doing it this way: 1- interpolate to a fine grid 2- plot points at each grid intersection of transparency inversely proportional to abundance 3- blur/fog a bit each point to create the general impression of a cloud So far I am stuck on 3 but maybe there is a better overall solution. Here is some code that reads the result of the interpolation on a coarse grid and plots it: # read a set of gridded data points in 3D d = read.table(http://dl.dropbox.com/u/1047321/R/test3Ddata.txt;, header=T) # plot library(rgl) spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05) And here is a version that actually performs the interpolation a random set of points in 3D through kriging in case you want to try with increase precision. # create a set of random data points in 3D n = 50 data3D = data.frame(x = runif(n), y = runif(n), z = runif(n), v = rnorm(n)) # do 3d interpolation via kriging library(gstat) coordinates(data3D) = ~x+y+z range1D = seq(from = 0, to = 1, length = 10) grid3D = expand.grid(x = range1D, y = range1D, z = range1D) gridded(grid3D) = ~x+y+z res3D = krige(formula = v ~ 1, data3D, grid3D, model = vgm(1, Exp, .2)) # convert the result to a data.frame d = as.data.frame(res3D) # compute transparency (proportional to the interpolated value) maxD = max(d$var1.pred) minD = min(d$var1.pred) alpha = (d$var1.pred - minD)/(maxD - minD) # reduce maximum alpha (all points are semi-transparent) alpha = alpha/5 # plot library(rgl) spheres3d(d$x, d$y, d$z, alpha=alpha, radius=0.05) I saw the fog effect but it seems to add a fog in the scene to increase depth. What I want is my scene to actually look like a fog. Thanks in advance for any help. Sincerely, JiHO --- http://maururu.net __ R-help@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. __ R-help@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.
Re: [R] Plotting a cloud/fog of variable density in rgl
Date: Mon, 22 Nov 2010 13:55:13 -0500 From: murdoch.dun...@gmail.com To: jo.li...@gmail.com CC: r-h...@stat.math.ethz.ch Subject: Re: [R] Plotting a cloud/fog of variable density in rgl On 22/11/2010 12:51 PM, JiHO wrote: Hi everyone, I want to plot a 3D interpolation of the concentration of aquatic organisms. My goal would be to have the result represented as clouds with a density proportional to the abundance of organisms, so that I could fly (well, swim actually ;) ) through the scene and see the patches here and there. Basically, I want to do something like this: http://www.youtube.com/watch?v=27mo_Y-aU-c but simpler and with only clouds. rgl doesn't make everything in OpenGL available. I'm not sure exactly how those clouds were done, but it wouldn't really be easy to do them in rgl. I think you can come closest to what you want within rgl by using sprites rather than rendering transparent spheres. See examples(sprites3d). If you only have 2 things with simple properties, namely point emitters as your organisms and a uniform concsntration of transparent scatters ( the fog) you can probably derive geometrical optics expressions for the ray trace results and just integrate those over your source distribution. This should be reasonably easy in R. I haven't been to siggraph since 1983 so can't help much but you can probably find analyitcal solutions for fog on google and just sum up your source distribution. I guess you could even do some wave optics etc as presumably the fog could be done as a function of wavelength just as easily. In any case, if you only have two basic things with simple disto should be reasonably easy to do in R with your own code. __ R-help@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.
