Just a small note in case it isn't obvious, its possible to treat the filename as in fopen, thus you can pass through the standard input from php like
 $descs = array (
 0 => array ("file", "php://stdin", "r"),
 1 => array ("pipe", "w"),
 2 => array ("pipe", "w")
 );
 $proc = proc_open ("myprogram", $descs, $fp);