[R] How to speed up int2bin conversion?

[Jonas Jägermeyr]

On 12/01/2011 02:46 PM, jim holtman wrote:
> If we assume that you are just convert 8 bits, here is one way with a
> table lookup.  If more than 8 bits, just partition the data and
> repeat.  This sets up a mapping table one time for the lookup.  Does
> 1M in 0.3 seconds on my computer; is this fast enough?
>
>> # initialize a matrix with 8 bit binary values
>> # one time
>> require(bitops)
>> b2c<- character(256)
>> for (i in 0:255){
> +     b2c[i + 1]<- sprintf("%1d%1d%1d%1d%1d%1d%1d%1d"
> +         , bitAnd(i, 0x80) != 0
> +         , bitAnd(i, 0x40) != 0
> +         , bitAnd(i, 0x20) != 0
> +         , bitAnd(i, 0x10) != 0
> +         , bitAnd(i, 0x8) != 0
> +         , bitAnd(i, 0x4) != 0
> +         , bitAnd(i, 0x2) != 0
> +         , bitAnd(i, 0x1) != 0
> +         )
> + }
>> # create vector with 1M values
>> x<- as.integer(1:1e6)
>>
>> int2bin<- function(val)
> + {
> +     b2c[bitAnd(val, 0xff) + 1]
> + }
>> system.time(int2bin(x))
>     user  system elapsed
>     0.31    0.00    0.32
>
> On Thu, Dec 1, 2011 at 7:14 AM, Jonas Jägermeyr<jonasjae at pik-potsdam.de>  wrote:
>> Dear R-help members,
>>
>> I'm processing a large amount of MODIS data where quality assessment
>> information is stored as an integer value for each pixel. I have to
>> converted this number to an 8 digit binary flag to get access to the
>> stored quality code (e.g. in2bin(165,8) = 1 0 1 0 0 1 0 1).
>>
>> Unfortunately, I did not manage to find a package providing a fast
>> function to do so. I need to run this on millions of pixels and thus
>> wrote the following function.
>>
>> int2bin<- function(x,ndigits){
>>      base<- array(NA, dim=c(length(x), ndigits))
>>      for(q in 1:ndigits){
>>            base[, ndigits-q+1]<- (x %% 2)
>>            x<- (x %/% 2)
>>        }
>>      bin<- apply(base,1,paste,collapse="")
>>      return(bin)
>> }
>>
>> Since it is still slow, I have to find a way to express this more
>> elegantly. I'd really appreciate any help.
>>
>> Thanking you, with best regards
>>
>> Jonas Jägermeyr
>>
>> Potsdam Institute for Climate Impact Research
>> Research Domain II
>>
>>         [[alternative HTML version deleted]]
>>
>>
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>>
>
>
Great Jim! Thanks a lot. New way of thinking, appreciated.
I also need 16 and 32 bit flags and hence I just added those two lines:

int2bin16<- function(val) {
     paste(int2bin(val%/%256),int2bin(val),sep="")
}

int2bin32<- function(val) {
     
paste(int2bin(val%/%256^3),int2bin(val%/%256^2),int2bin(val%/%256),int2bin(val),sep="")
}

Best,
Jonas Jägermeyr

Potsdam Institute for Climate Impact Research
Research Domain II