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
                                                  Flat 3
PGP: http://www.infracaninophile.co.uk/pgpkey     Ramsgate
                                                  Kent, CT11 9PW

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