Profiling a script in python is as easy as calling:

python -m cProfile myscript.py

see also: http://docs.python.org/2/library/profile.html#module-cProfile

the problem is that sometimes the code you want to profile deep in InaSAFE. You can still get nice cProfiles by replacing the original call with a call to cProfile.runctx()

so:

self.preparePolygonLayerForAggr(theClippedHazardFilename, myHazardLayer)

would become:

cProfile.runctx('self.preparePolygonLayerForAggr(theClippedHazardFilename, myHazardLayer)', globals(), locals())

see also http://stackoverflow.com/questions/1031657/profiling-self-and-arguments-in-python

You can put a raise statement right after the runctx call so the execution is stopped and you can see your cProfile results in the console