I suspect that "junk" (the four bytes after the 2nd record marker), read as a 4-byte integer instead of four 1-byte integers, is the number of bytes of data following it. Its value in your example is 18920 = 8 * 43 * 55, where 43 and 55 are two integers in the header, probably the dimensions of the array containing the double precision data.
Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf > Of William Dunlap > Sent: Monday, June 18, 2012 6:43 PM > To: kapo coulibaly; r-help@r-project.org > Subject: Re: [R] Help with readBin > > 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:kmcou...@gmail.com] > Sent: Monday, June 18, 2012 5:55 PM > To: William Dunlap; r-help@r-project.org > 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 > <wdun...@tibco.com<mailto:wdun...@tibco.com>> wrote: > Did you ever send the output of dput to R-help? > On Thu, May 3, 2012 at 5:00 PM, William Dunlap > <wdun...@tibco.com<mailto:wdun...@tibco.com>> 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:kmcou...@gmail.com<mailto:kmcou...@gmail.com>] > Sent: Monday, June 18, 2012 5:35 PM > To: William Dunlap > Cc: r-help@r-project.org<mailto:r-help@r-project.org> > > 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 > <wdun...@tibco.com<mailto:wdun...@tibco.com>> 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: r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org> > > [mailto:r- > help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>] On Behalf > > Of kapo coulibaly > > Sent: Thursday, May 03, 2012 10:57 AM > > To: r-help@r-project.org<mailto:r-help@r-project.org> > > 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 > > <murdoch.dun...@gmail.com<mailto:murdoch.dun...@gmail.com>>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]] > > > > ______________________________________________ > > R-help@r-project.org<mailto:R-help@r-project.org> 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. > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org 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. ______________________________________________ R-help@r-project.org 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.
