Is it possible to write the output of the profiler to a log via php functions?

yes if you mean line profiler.
In this case you can add script in php.ini that will run _after_ each request. In this script you'll collect profiler results and send them wherever you want.
API is not well documented, but you'll figure out how it works -- it's very simple
Start here: http://forum.nusphere.com/howto-get-results-from-dbg-get-profiler-results-t1848.html

Hi Dimitri,
Thanks for your info but I don't understand where in your example a script is called from php.ini that then writes the log. I made the settings in php.ini and call the following in my php script.

$result remains empty though. How do I get the profiler data?

$result = dbg_get_profiler_results(); would do.
Note: you still need IDE running and you still need to run HTTP request or CLI command to launch your script with DBGSESSID argument to tell debugger you want to run profiler.

Thanks for the tip, that works