arraytake for extracting subarrays from multidimensional arrays

Note that it can also be done like with do.call:

a <- array(1:24, 2:4)
L <- list(TRUE, 1:3, c(4, 2))
do.call("[", c(list(a), L))

On 10/19/06, Balaji S. Srinivasan <balajis at stanford.edu> wrote:

Hi,

I recently encountered a problem with array subsetting and came up  
with a
fix. Given an array of arbitrary dimensions, in which the number of
dimensions is only known at runtime, I wanted to extract a  
subarray. The
main issue with doing this is that in order to extract a subarray  
from an
array of (say) 4 dimensions you usually specify something like this

a.subarray <- a[,c(4,2),1:5,]

However, if your code needs to handle an array with an arbitrary  
number of
dimensions then you can't hard code the number of commas while  
writing the
code. (Regarding motivation, the reason this came up is because I  
wanted to
do some toy problems involving conditioning on multiple variables  
in a
multidimensional joint pmf.)

I looked through commands like slice.index and so on, but they  
seemed to
require reshaping and big logical matrix intermediates, which were  
not
memory efficient enough for me. apltake in the magic package was  
the closest
but it only allowed subsetting of contiguous indices from either  
the first
or last element in any given dimension. It was certainly possible  
to call
apltake multiple times to extract arbitrary subarrays via  
combinations of
index intervals for each dimension, and then combine them with  
abind as
necessary, but this did not seem elegant.

Anyway, I then decided to simply generate code with parse and  
eval. I found
this post by Henrik Bengtsson which had the same idea:

http://tolstoy.newcastle.edu.au/R/devel/05/11/3266.html

I just took that code one step further and put together a utility  
function
that I think might be fairly useful. I haven't completely  
robustified it
against all kinds of pathological inputs, but if there is any  
interest from
the development team it would be nice to add an error-checked  
version of
this to R (or I guess I could keep it in a package).


Simple usage example:
------

source("arraytake.R")
a <- array(1:24,c(2,3,4))

a[,1:3,c(4,2)] ##This invocation requires hard coding the number of

dimensions of a
, , 1

    [,1] [,2] [,3]
[1,]   19   21   23
[2,]   20   22   24

, , 2

    [,1] [,2] [,3]
[1,]    7    9   11
[2,]    8   10   12

arraytake(a,list(NULL,1:3,c(4,2))) ##This invocation does not, and

produces the same result
, , 1

    [,1] [,2] [,3]
[1,]   19   21   23
[2,]   20   22   24

, , 2

    [,1] [,2] [,3]
[1,]    7    9   11
[2,]    8   10   12



Code below:
--------
arraytake <- function(x,indlist) {

 #Returns subarrays of arbitrary dimensioned arrays
 #1) Let x be a multidimensional array with an arbitrary number of
dimensions.
 #2) Let indlist be a list of vectors. The length of indlist is  
the same as
the number of
 #dimensions in x. Each element of the indlist is a vector which  
specifies
which
 #indexes to extract in the corresponding dimension. If the  
element of the
indlist is
 #NULL, then we return all elements in that dimension.

 #The main way this works is by programmatically building up a comma
separated argument to "[" as a string
 #and then simply evaluating that expression. This way one does  
not need to
specify the number of
 #commas.

 if(length(dim(x)) != length(indlist)) {
   return();  #we would put some error message here in production  
code
 }

 #First build up a string w/ indices for each dimension
 d <- length(indlist);  #number of dims
 indvecstr <- matrix(0,d,1);
 for(i in 1:d) {
   if(is.null(indlist[[i]])) {
     indvecstr[i] <- "";
   } else{
     indvecstr[i] <-
paste("c(",paste(indlist[[i]],sep="",collapse=","),")",sep="")
   }
 }

 #Then build up the argument string to "["
 argstr <- paste(indvecstr,sep="",collapse=",")
 argstr <- paste("x[",argstr,"]",sep="")

 #Finally, return the subsetted array
 return(eval(parse(text=argstr)))
}







--
Dr. Balaji S. Srinivasan
Stanford University
Depts. of Statistics and Computer Science
318 Campus Drive, Clark Center S251
(650) 380-0695
balajis at stanford.edu
http://jinome.stanford.edu

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