reading select values from a binary file

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