Re: editing a binary file

[Matthew Seaman]

Anton Shterenlikht wrote:

On Fri, Dec 18, 2009 at 02:09:58AM +0100, Rolf Nielsen wrote:

Anton Shterenlikht wrote:

I'm creating binary files in fortran.
Fortran adds 4 byte record delimiters at the beginning
and the end of each record, which, in the case of a binary
file, is just at the beginning and at the end of the file.
I need to delete these record delimiters, because the
software I use to visualise the binary files interprets
them as data. But I don't know how. I've looked at
hexdump and od, but those are only dumping (I think)
file contents, and I cannot see how to edit a file with them.

Any advice?

many thanks
anton

Hello Anton,

My bet would be /usr/ports/editors/hexedit. Been a while since I've used it, but AFAIR, it has a curses or a curses like interface, and it's fairly simple to use, yet sufficiently powerful for most normal binary editing. If you want a GUI, I believe gnome (and probably KDE as well) has its own hex editor.

thank you. hexedit does the job on small files, but is quite
clunky. If I've a xGB file and I need to delete the first and
the last record, this becomes quite hard, if at all possible.

I didn't appreciate it's not that simple.

Perhaps I can read a file with C and write back? I can't
remember if C supports binary files, and whether it
also writes some record delimiters.

Sure, you can write a fairly short C program to do this.  In fact,
it's pretty easy in perl too:

#!/usr/bin/perl -w

use Fcntl;
use constant BUFFSIZ => 4096;

for my $file (@ARGV) {
   my $buffer     = '';
   my $bytes_read = 0;

   sysopen INFILE, $file, O_RDONLY
       or die "Failed to open file $file for reading -- $!\n";
   sysseek INFILE, 4, 0;  # skip first 4 bytes
   sysopen OUTFILE, "${file}.out", O_WRONLY|O_CREAT
       or die "Failed to open file ${file}.out for writing -- $!\n";
   while ( $bytesread = sysread INFILE, $buffer, BUFFSIZ, 0 ) {
       # If we don't read 4096 bytes, try a second read: if this
       # returns zero, then we're at EOF
        if ( $bytes_read < BUFFSIZ ) {
            my $offset = $bytes_read;
           $bytes_read = sysread INFILE, $buffer, BUFFSIZ, $offset;

           if ( $bytes_read == 0 ) {
               # Trim the last 4 bytes
               substr ($buffer, -4) = ''; # Trim off last 4 bytes
           }
        }
       syswrite OUTFILE, $buffer;
   }
   close INFILE;
   close OUTFILE;
}


Untested, and needs more error checking around those sysread()s and syswrite()s,
but it should give you the general idea.

        Cheers,

        Matthew

--
Dr Matthew J Seaman MA, D.Phil.                   7 Priory Courtyard
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