Re: [Rd] inline C/C++ in R: question and suggestion
That is actually a (rare) case that can be completely vectorized: Thanks for the vectorization solution. I really like the idea! Except for the fact that it's forcing the use of C++ which adds unnecessary overhead :P I can make it optional. I was just thinking that C++ would be more general than C. I was also asked to create a .C interface, which to me has the only difference that one needs to preallocate the result. But the same is easy to implement by pre-allocating an R variable and passing it as an argument with NULL return. 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 :) It would be nice, but I doubt it is feasible at all and if yes, the overhead will be enormous, especially weighted by the number of people using it. However, what I would consider reasonable is to have such an inline interface to more than just C and C++. There is something for Ruby I think, but one could think of generalizing it somehow. Best, Oleg __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] inline C/C++ in R: question and suggestion
I think the only way this would affect your package is that you need to be able to handle embedded newlines in strings, but I can't see why you wouldn't be able to do that automatically. That would be no problem if there were such a thing. As for now, I think the Deepayan's solution for multi line string input is quite elegant. You might want to allow a list of signatures and code chunks to be passed to the compiler, producing a list of functions to evaluate them, all compiled into one DLL. Reasonable and doable. Will do using setMethod implementation. Thanks, Oleg -- Dr Oleg Sklyar * EBI/EMBL, Cambridge CB10 1SD, England * +44-1223-494466 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] inline C/C++ in R: question and suggestion
This is a question and maybe an announcement.
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.
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. It is a draft
and I will be happy to improve it (especially comments on how to ensure
that the shared object is unloaded when the function is removed). In the
example below EBImage is not required, I use randomly generated values
instead of images, but the output it quite obvious. After installing
inline the example should just work by copy-pasting.
Best and thanks in advance,
Oleg
code - character(17)
code[1] - SEXP res;
code[2] - int nprotect = 0, nx, ny, nz, x, y;
code[3] - PROTECT(res = Rf_duplicate(a)); nprotect++;
code[4] - nx = INTEGER(GET_DIM(a))[0];
code[5] - ny = INTEGER(GET_DIM(a))[1];
code[6] - nz = INTEGER(GET_DIM(a))[2];
code[7] - double sigma2 = REAL(s)[0] * REAL(s)[0], d2 ;
code[8] - double cx = REAL(centre)[0], cy = REAL(centre)[1], *data,
*rdata;
code[9] - for (int im = 0; im nz; im++) {
code[10] - data = (REAL(a)[im*nx*ny]); rdata =
(REAL(res)[im*nx*ny]);
code[11] - for (x = 0; x nx; x++)
code[12] -for (y = 0; y ny; y++) {
code[13] - d2 = (x-cx)*(x-cx) + (y-cy)*(y-cy);
code[14] - rdata[x + y*nx] = data[x + y*nx] * exp(-d2/sigma2);
code[15] - }}
code[16] - UNPROTECT(nprotect);
code[17] - return res;
library(inline)
funx - cfunction(signature(a=array, s=numeric, centre=numeric), code)
x - array(runif(50*50), c(50,50,1))
res - funx(a=x, s=15, centre=c(30,35))
image(res[,,1])
res - funx(x, 10, c(15,15))
x11(); image(res[,,1])
--
Dr Oleg Sklyar * EBI/EMBL, Cambridge CB10 1SD, England * +44-1223-494466
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Re: [Rd] inline C/C++ in R: question and suggestion
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
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Re: [Rd] inline C/C++ in R: question and suggestion
On 5/22/2007 1:59 PM, Oleg Sklyar wrote: This is a question and maybe an announcement. 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. This would be nice. One suggestion that probably doesn't affect your package: It would be even nicer if R incorporated something that Duncan Temple Lang suggested last year, namely a new kind of quoting that didn't need escapes in the string. He suggested borrowing triple quotes from Python; I suggested something more like heredocs as in shells or Perl, or like \verb in TeX, in case you wanted triple quotes in your C function. It would be nice to settle on something, so that instead of code[1] - SEXP res; code[2] - int nprotect = 0, nx, ny, nz, x, y; code[3] - PROTECT(res = Rf_duplicate(a)); nprotect++; code[4] - nx = INTEGER(GET_DIM(a))[0]; code[5] - ny = INTEGER(GET_DIM(a))[1]; one could use (for example): code - ''' SEXP res; int nprotect = 0, nx, ny, nz, x, y; PROTECT(res = Rf_duplicate(a)); nprotect++; nx = INTEGER(GET_DIM(a))[0]; ny = INTEGER(GET_DIM(a))[1]; ''' I think the only way this would affect your package is that you need to be able to handle embedded newlines in strings, but I can't see why you wouldn't be able to do that automatically. Another suggestion: You might want to allow a list of signatures and code chunks to be passed to the compiler, producing a list of functions to evaluate them, all compiled into one DLL. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] inline C/C++ in R: question and suggestion
On Tuesday 22 May 2007 3:52 pm, Duncan Murdoch wrote:
On 5/22/2007 1:59 PM, Oleg Sklyar wrote:
One suggestion that probably doesn't affect your package: It would be
even nicer if R incorporated something that Duncan Temple Lang suggested
last year, namely a new kind of quoting that didn't need escapes in the
string. He suggested borrowing triple quotes from Python; I suggested
something more like heredocs as in shells or Perl, or like \verb in TeX,
in case you wanted triple quotes in your C function. It would be nice
to settle on something, so that instead of
I second that. My favorite implementation of this is in Tcl, where curly
braces {} mean that the text they enclose is unmodified. Since language
constructs using them are normally balanced this is not an impediment.
One extremely useful application of this (aside from long strings) is
specifying inline data frames - I don't know how to do this otherwise.
I.e. something like:
A- scan.string({#
Id Value Mark
1 a 3
2 b 4
# })
best
Vladimir Dergachev
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