You didn't give much of a description of what sort of numbers you expected
in the header so this is pretty much a guess. However, by reading the tail of
the file with offsets 0 through 7 bytes we get numbers in the 30-40 range for
an offset of 4 bytes. I called that field "junk" below and placed it so that
the
two recordMarker fields were the same (52 decimal). Do the numbers in the
header look right?
f <- function (filename)
{
con <- file(filename, "rb")
on.exit(close(con))
rbl <- function(...) readBin(..., endian = "little")
recordMarkerA <- rbl(con, what = "integer", size = 4, n = 1)
twoIntegers <- rbl(con, what = "integer", size = 4, n = 2)
twoDoubles <- rbl(con, what = "numeric", size = 8, n = 2)
oneString <- rawToChar(rbl(con, what = "raw", size = 1, n = 16))
threeIntegers <- rbl(con, what = "integer", size = 4, n = 3)
recordMarkerB <- rbl(con, what = "integer", size = 4, n = 1)
junk <- rbl(con, what = "raw", size = 1, n = 4)
# the 100 below should be (file.info(filename)$size - headerSize)/8
doubles <- rbl(con, what = "numeric", size = 8, n = 100)
list(recordMarkerA = recordMarkerA, twoIntegers = twoIntegers,
twoDoubles = twoDoubles, oneString = oneString, threeIntegers =
threeIntegers,
recordMarkerB = recordMarkerB, junk = junk, doubles = doubles)
}
> f(tf)
$recordMarkerA
[1] 52
$twoIntegers
[1] 1 1
$twoDoubles
[1] 1 1
$oneString
[1] " HEAD"
$threeIntegers
[1] 43 55 1
$recordMarkerB
[1] 52
$junk
[1] e8 49 00 00
$doubles
[1] 33.674 34.272 34.736 35.098 35.378 35.628
[7] 35.838 36.046 36.324 36.604 36.856 37.112
[13] 37.398 37.694 38.008 38.364 38.742 39.134
[19] 39.494 39.844 40.128 40.372 40.562 40.712
[25] 40.818 40.880 40.900 40.882 40.830
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
From: kapo coulibaly [mailto:[email protected]]
Sent: Monday, June 18, 2012 5:55 PM
To: William Dunlap; [email protected]
Subject: Re: [R] Help with readBin
No. But here it is:
c(52L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, -16L, 63L, 0L, 0L, 0L, 0L, 0L, 0L, -16L, 63L, 32L,
32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 72L, 69L,
65L, 68L, 43L, 0L, 0L, 0L, 55L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 52L,
0L, 0L, 0L, -24L, 73L, 0L, 0L, -125L, -64L, -54L, -95L, 69L,
-42L, 64L, 64L, -119L, 65L, 96L, -27L, -48L, 34L, 65L, 64L, -111L,
-19L, 124L, 63L, 53L, 94L, 65L, 64L, 6L, -127L, -107L, 67L, -117L,
-116L, 65L, 64L, -86L, -15L, -46L, 77L, 98L, -80L, 65L, 64L,
-86L, -15L, -46L, 77L, 98L, -48L, 65L, 64L, 37L, 6L, -127L, -107L,
67L, -21L, 65L, 64L, -39L, -50L, -9L, 83L, -29L, 5L, 66L, 64L,
-74L, -13L, -3L, -44L, 120L, 41L, 66L, 64L, 90L, 100L, 59L, -33L,
79L, 77L, 66L, 64L, 33L, -80L, 114L, 104L, -111L, 109L, 66L,
64L, 117L, -109L, 24L, 4L, 86L, -114L, 66L, 64L, 109L, -25L,
-5L, -87L, -15L, -78L, 66L, 64L, 70L, -74L, -13L, -3L, -44L,
-40L, 66L, 64L, 27L, 47L, -35L, 36L, 6L, 1L, 67L, 64L, 59L, -33L,
79L, -115L, -105L, 46L, 67L, 64L, -27L, -48L, 34L, -37L, -7L,
94L, 67L, 64L, -2L, -44L, 120L, -23L, 38L, -111L, 67L, 64L, -84L,
28L, 90L, 100L, 59L, -65L, 67L, 64L, 121L, -23L, 38L, 49L, 8L,
-20L, 67L, 64L, -86L, -15L, -46L, 77L, 98L, 16L, 68L, 64L, 86L,
14L, 45L, -78L, -99L, 47L, 68L, 64L, 14L, 45L, -78L, -99L, -17L,
71L, 68L, 64L, 66L, 96L, -27L, -48L, 34L, 91L, 68L, 64L, 98L,
16L, 88L, 57L, -76L, 104L, 68L, 64L, 113L, 61L, 10L, -41L, -93L,
112L, 68L, 64L, 51L, 51L, 51L, 51L, 51L, 115L, 68L, 64L, 55L,
-119L, 65L, 96L, -27L, 112L, 68L, 64L, 10L, -41L, -93L, 112L,
61L, 106L, 68L, 64L, -53L, -95L, 69L, -74L)
On Mon, Jun 18, 2012 at 8:39 PM, William Dunlap
<[email protected]<mailto:[email protected]>> wrote:
Did you ever send the output of dput to R-help?
On Thu, May 3, 2012 at 5:00 PM, William Dunlap
<[email protected]<mailto:[email protected]>> wrote:
You can do the following to allow others to recreate your problem.
yourFileBytes <- readBin("yourFile", what="integer", size=1, n=300) # is 300
bytes enough to see the problem?
dput(yourFileBytes)
Put the output of dput(yourFileBytes) in your mail.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com<http://tibco.com>
From: kapo coulibaly [mailto:[email protected]<mailto:[email protected]>]
Sent: Monday, June 18, 2012 5:35 PM
To: William Dunlap
Cc: [email protected]<mailto:[email protected]>
Subject: Re: [R] Help with readBin
I still haven't found a working solution. Is it allowed to attach a file so
that somebodyelse can reproduce the problem?
On Thu, May 3, 2012 at 5:00 PM, William Dunlap
<[email protected]<mailto:[email protected]>> wrote:
You can do the following to allow others to recreate your problem.
yourFileBytes <- readBin("yourFile", what="integer", size=1, n=300) # is 300
bytes enough to see the problem?
dput(yourFileBytes)
Put the output of dput(yourFileBytes) in your mail. Someone can (and you
should)
recreate the problem with
bytes <- ... copy 'n paste the printout of dput(bytes) here ...
tf <- tempfile()
stopifnot(is.integer(bytes) && all(abs(bytes)<=128)) # to make sure bytes was
copied correctly
writeBin(bytes, con=tf, size=1)
Then show just the commands needed to read a couple of rows of your file, along
with
the expected output, as precisely and you can. E.g.,
con <- file(tf, "rb")
readBin(con, what="integer", size=4, n=2) # expect 3 then something less than
10
readBin(con, what="numeric", size=8, n=3) # expect 2 numbers in range (0, 32]
then 2.57
...
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com<http://tibco.com>
> -----Original Message-----
> From: [email protected]<mailto:[email protected]>
> [mailto:[email protected]<mailto:[email protected]>] On
> Behalf
> Of kapo coulibaly
> Sent: Thursday, May 03, 2012 10:57 AM
> To: [email protected]<mailto:[email protected]>
> Subject: Re: [R] Help with readBin
>
> I believe here is the structure of the file I'm trying to read:
> record marker (4 bytes), 2 integers (4 bytes each), 2 doubles (8 bytes
> each), one string (16 bytes or 16 characters), 3 integers (4 bytes each), 1
> record marker (4 bytes) and a big array of doubles (8 bytes each).
> Everything in the file is read correctly except for the doubles.
> If any indication, I've read similar file before with readBin the only
> difference is this one was created with a code compiled with gfortran in
> linux 64 bit. I was able to read the same output binary file when the
> fortran source code was compiled in windows xp 32 bit. The values I'm
> expecting should be between 0 and about 32.
>
>
>
>
> The code I used is:
>
>
>
> # Loading Required libraries
> library(tcltk)
>
> # Tk inputbox function
> inputBox<-function() {
> tt<-tktoplevel()
> Zmin<-tclVar("0")
> Zmax<-tclVar("0")
> dZ<-tclVar("0")
> entry.Zmin<-tkentry(tt,width="20",textvariable=Zmin)
> entry.Zmax<-tkentry(tt,width="20",textvariable=Zmax)
> entry.dZ<-tkentry(tt,width="20",textvariable=dZ)
> lbl.Zmin<-tklabel(tt,text="Number of layers")
> lbl.Zmax<-tklabel(tt,text="Number of Stress Periods")
> lbl.dZ<-tklabel(tt,text="dZ")
> tkgrid(lbl.Zmin,entry.Zmin)
> tkgrid(entry.Zmin)
> tkgrid(lbl.Zmax,entry.Zmax)
> tkgrid(entry.Zmax)
> #tkgrid(lbl.dZ,entry.dZ)
> #tkgrid(entry.dZ)
>
> OnOK <- function()
> {
> # NameVal <- c(tclvalue(Zmin),tclvalue(Zmax),tclvalue(dZ))
> tkdestroy(tt)
> }
> OK.but <-tkbutton(tt,text=" OK ",command=OnOK)
> # tkbind(entry.Name, "<Return>",OnOK)
> tkgrid(OK.but,columnspan=3)
> tkfocus(tt)
> tkwait.window(tt)
> res<-as.numeric(c(tclvalue(Zmin),tclvalue(Zmax)))#,tclvalue(dZ)))
> return(res)
> }
>
> ########################################################################
> ########
> # Main program
> ########################################################################
> ########
>
> # Model Parameters input (number of layers and stress periods)
> param<-inputBox()
>
> # Select and open Modflow Binary file for reading
> fich<-tclvalue(tkgetOpenFile(title="Modflow Binary File",filetypes="{{hds
> binary Files} {.hds}} {{All files} *}"))
> zz <- file(fich, "rb")
>
> # Cycling thru time steps and layers
> for (k in 1:param[2]) {
> for (i in 1:param[1]) {
> readBin(zz,what="numeric",n=1,size=4) # record marker typical of
> fortran access="sequential" in gfortran
> readBin(zz,what="integer",n=2,size=4)->N1
> readBin(zz,what="double",n=2,size=8)->N2
> readChar(zz,16)->txt1
> print(txt1)
> readBin(zz,what="integer",n=3,size=4)->N3
> tnber<-N3[1]*N3[2]
> readBin(zz,what="integer",n=1,size=4) # record marker typical of
> fortran access="sequential" in gfortran
> readBin(zz,what=real(),n=tnber,size=4)->N4
> readBin(zz,what="integer",n=2,size=4) # record marker typical of
> fortran access="sequential" in gfortran
> print(N4[1:10])
>
>
> }
>
> }
>
> close(zz)
>
> On Thu, May 3, 2012 at 1:26 PM, Duncan Murdoch
> <[email protected]<mailto:[email protected]>>wrote:
>
> > On 03/05/2012 12:41 PM, kapo coulibaly wrote:
> >
> >> I'm trying to read a binary file created by a fortran code using readBin
> >> and readChar. Everything reads fine (integers and strings) except for
> >> double precision numbers, they are read as huge or very small number
> >> (1E-250,...). I tried various endianness, swap, But nothing has worked so
> >> far.
> >> I also tried on R 64 bit for linux and windows (R 2.14) and R 2.11 on
> >> windows XP 32 bit.
> >> Any help would be appreciated.
> >>
> >
> > As I wrote to someone else with a similar problem a couple of weeks ago:
> >
> > You need to see what's in the file. The hexView package can dump it in
> > various formats; see example(viewFormat) for a couple.
> >
> > Duncan Murdoch
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [email protected]<mailto:[email protected]> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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