Oleg, On May 22, 2007, at 1:59 PM, Oleg Sklyar wrote:
> We've been discussing in the group that it would be nice to have a > mechanism for something like "inline" C/C++ function calls in R. I > do not want to reinvent the wheel, therefore, if something like > that already exists, please give me a hint -- I could not find > anything. If not, here is a working solution, please criticise so I > could improve it. > > Example: I work on images (Bioconductor:EBImage) and just came to a > point where I need to apply certain functions to image data, which > are grey scale intensities in the range [0,1]. Assume I want to > transform my image data from I(x,y,i) to exp(-(d/s)^2)*I(x,y,i), > where I is the original intensity in dependence on coordinates x,y > and frame i; s is a given value and d^2=(x-centre.x)^2+(y-centre.y) > ^2 for a given centre. Trying an R loop will run forever already on > moderate image sizes as I do not see how to vectorize it. > That is actually a (rare) case that can be completely vectorized: d=(cx-rep(1:dim(I)[1],dim(I)[2]*dim(I)[3]))^2+(cy-rep(1:dim(I) [2],each=dim(I)[1],times=dim(I)[3]))^2 I=I*exp(-(d/s^2)) Clearly the drawback is the use of memory, but you could vectorize per frame if you wish. At any rate it's not that slow anyway: > I=array(runif(100*100*10),c(100,100,10)) > system.time({d=(cx-rep(1:dim(I)[1],dim(I)[2]*dim(I)[3]))^2+(cy-rep (1:dim(I)[2],each=dim(I)[1],times=dim(I)[3]))^2;I=I*exp(-(d/s^2))}) user system elapsed 0.022 0.010 0.032 > system.time(funx(I,15,c(30,35))) user system elapsed 0.008 0.001 0.010 Of course C wins, no doubt about that :). > Now, below is the solution using the "inline" C code, completely in > R and runs instantly. I created a small package "inline" that > simply encapsulates a quite simple function "cfunction". The > package source is available from http://www.ebi.ac.uk/~osklyar/ > inline -- please give it a try and I would be happy to hear your > comments, both on already existing implementations for "inline" > calls and on the current one. I really like the idea! Except for the fact that it's forcing the use of C++ which adds unnecessary overhead :P I'd like a configurable extension [including .m] and the ability to prepend functions as code. What would be very useful now is a set of tools that would allow you to construct the source with R commands, so that you could compute on it, edit it etc. That would be really cool ... you could even imagine compiling a very restricted set of R into C code ... yes, I know I'm dreaming ;) Thanks for the good idea! Cheers, Simon ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel