Solved by 5had3z in post #2 
              
              
                Yeah so if I chunk it down into slices of 999 with a mask each iteration is less than a millisecond, and after looping over all of them, it results in a factor of 10 reduction in overall time spent (max time 40ms, usually ~10ms). 
I found a few magic numbers with SummaryOps.cu:  THRESH_NUMBER_BINS_F…