[SciPy-User] line_profiler and for-loops !?

Dag Sverre Seljebotn dagss@student.matnat.uio...
Tue Mar 16 03:49:11 CDT 2010

Sebastian Haase wrote:
> Hi,
> I was starting to use Robert's line_profiler. I seems to work great,
> and I already found one easy way do half my execution time.
> But now it claims that 33% of the time is spent (directly) in the
> "for"-line and another 36% in a very simple "if"-line. See parts of
> the output here:
> <snip>
> Function: doTracing at line 1135
> Total time: 23.9171 s
> Line #      Hits         Time  Per Hit   % Time  Line Contents
> ==============================================================
> <snip>
>   1185                                                       # iterate
> over all tracks, and find close points
>   1186   3853362      8024186      2.1     33.5              for
> tracki,track in enumerate(self.tracks):
>   1187   3853063      8639273      2.2     36.1                  if
> self.tracks_tLast[tracki] == t-1:
>   1188
>                   # track went on until t-1 (so far)
>   1189
>                   #    --  otherwise, skip "old" tracks
>   1190     62150       130277      2.1      0.5
>    pi_t_1 = track[-1] # index in last time section
> <snip>
> (The object of the function is to connect closest points found in an
> image sequence into tracks connecting the points by shortest steps.)
> Anyhow, my question is, is this just an artifact of line_profiler, or
> is the fact that those two lines are hit almost 4e6 times really
> resulting in more than 50% of the time being spent here !?
> (Calculating the actual Euclidean distance matrix over all point pairs
> takes supposedly only 15% of the time, for comparison).
> I tried to separate out the "enumerate(self.tracks)" into a separate
> line before the "for"-line, but the time spent was still unchanged on
> the "for".
> Does this mean "python is slow" here - and I should try cython (which
> i have never done so far ...) ?
Well, that for-line contains enumerate, which is a very non-trivial 
thing (a generator) and results in several functions calls being made. 
And that if-test line contains self.tracks_tLast[...] which is rather 
costly (one attribute lookup to get tracks_tLast (which you can put in a 
function local variable for a minor speedup), and then element indexing 
certainly isn't free either).

At least for the latter, put the value lookup into a temporary variable 
in a seperate line to get better profiling results.

But at one point the running times are so low that line-profiling gets 
very inaccurate, and if you still need more speed that's when you want 
to use Cython. If these lookups indeed dominate, Cython should give good 

Dag Sverre

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