[R-sig-Geo] reading select values from a binary file

[Michael Sumner]

?seek

The "where" argument is an offset in bytes, so you need to offet 2
bytes for each of your integers:

writeBin(1:20,"test.bip",size=2,endian="big")
cc <- file("test.bip","rb")
readBin(cc,"integer",n=1,size=2,endian="big")
seek(cc, 26)
readBin(cc,"integer",n=1,size=2,endian="big")
## [1] 14
close(cc)

Use seek(cc) to find the current offset on the connection.

HTH

On Thu, Dec 17, 2009 at 5:12 AM, Jonathan Thayn <jthayn at ilstu.edu> wrote:
> I tried using the seek() function, but it did not work as I thought it would. Perhaps I have done something wrong:
>
>> writeBin(1:20,"desktop/test.bip",size=2,endian="big")
>> cc <- file("desktop/test.bip","rb")
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 1
>> seek(cc,13)
> [1] 2
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 1792 #this is not correct
>> seek(cc,0)
> [1] 15
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 1 #the seek(cc,0) seems to have reset it
>> flush(cc)
>> seek(cc,6)
> [1] 2
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 4 #this is not the sixth number
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 5
>> flush(cc)
>> seek(cc,12)
> [1] 10
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 7 #this is not the twelfth number
>> flush(cc)
>> seek(cc,1)
> [1] 14
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 256
>> seek(cc,0)
> [1] 3
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 1
>> seek(cc,18)
> [1] 2
>> readBin(cc,"integer",n=1,size=2,endian="big")
> [1] 10
>
>
> I tried the readBinFragments() function in the R.utils package and it works, so long as I use a seek(cc,0) between calls:
>
> readBinFragments(cc,"integer",idxs=c(2,6,7,13,19),size=2,endian="big")
> [1]  2  6  7 13 19
>> readBinFragments(cc,"integer",idxs=c(4,9,12),size=2,endian="big")
> [1] 0 0 0
>> flush(cc)
>> readBinFragments(cc,"integer",idxs=c(4,9,12),size=2,endian="big")
> [1] 0 0 0
>> seek(cc,0)
> [1] 52
>> readBinFragments(cc,"integer",idxs=c(4,9,12),size=2,endian="big")
> [1]  4  9 12
>
>
> Am I using seek() incorrectly?
>
>
>
> Jonathan B. Thayn
>
>
>
>
> On Dec 9, 2009, at 12:33 PM, Barry Rowlingson wrote:
>
>> On Wed, Dec 9, 2009 at 6:20 PM, rick reeves <reeves at nceas.ucsb.edu> wrote:
>>> Hello All:
>>> Faced with a similar challenge, and NOT wanting to resort to writing a C
>>> language function
>>> employing fseek(), I just used two readBin calls: One to read (and
>>> implicitly discard) data up
>>> to the spot I actually wanted to read, and a second call to read the desired
>>> information.
>>> here is a code sample:
>>>
>>>                     fileCon = file(sTsFileName,"rb")
>>> #
>>> # Offset has been calculated above: number of NumericByte-sized elements
>>> preceeding
>>> # the data of interest.
>>> #
>>>                     if (iOffset > 0)
>>>                     {
>>>
>>>                        TestVec = readBin(fileCon,numeric(),size =
>>> iNumericBytes,n=iOffset)
>>>                     }
>>>                       dTimeSeries = readBin(fileCon,numeric(),size =
>>> iNumericBytes,n=iNumElements)                     close(fileCon)
>>>
>>> Crude, but effective. I WIS that we could add a seekBin() function that
>>> positions the file pointer
>>> to the desired spot.
>>>
>>
>> The R seek function does this. I hadn't tested it when I posted,
>> hoping the original poster would work it from my message. So I just
>> now tested it:
>>
>> I created a file with ascii a to z in, and then:
>>
>>> con = file("file.tst","rb")
>> # jump to 13th letter:
>>> seek(con,13)
>> [1] 0
>> # read it:
>>> readBin(con,what="raw",n=1)
>> [1] 6e     # thats ascii 'n'
>> # jump back:
>>> seek(con,1)
>> [1] 14 # returns where we were, we've now moved...
>>> readBin(con,what="raw",n=1)
>> [1] 62  # ascii 'b'. Things start at zero....
>>
>> Is that what you are trying to do?
>>
>> Barry
>
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