[R] Help with readBin

[Duncan Murdoch]

On 03/05/2012 1:57 PM, kapo coulibaly wrote:
>   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 first two doubles read properly as 1, and the next one as 33.674, 
when I follow your description above on the dump you sent me 
privately.   I'm on a system with endian="little"; you might want to 
specify that explicitly in your readBin calls.

And please, in future, spend some time making your questions easier to 
answer:  put the dump in the public message.  Don't post irrelevant 
code, extract just the bit that's doing the reading.

Duncan Murdoch

>
>
>
>
> 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.duncan at 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 at 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.