user248237dfsf user248237dfsf - 1 year ago 59
Python Question

Speeding up pairing of strings into objects in Python

I'm trying to find an efficient way to pair together rows of data containing integer points, and storing them as Python objects. The data is made up of

coordinate points, represented as a comma separated strings. The points have to be paired, as in
(x_1, y_1), (x_2, y_2), ...
etc. and then stored as a list of objects, where each point is an object. The function below
generates this example data:

def get_data(N=100000, M=10):
import random
data = []
for n in range(N):
pair = [[str(random.randint(1, 10)) for x in range(M)],
[str(random.randint(1, 10)) for x in range(M)]]
row = [",".join(pair[0]),
return data

The parsing code I have now is:

class Point:
def __init__(self, a, b):
self.a = a
self.b = b

def test():
import time
data = get_data()
all_point_sets = []
time_start = time.time()
for row in data:
point_set = []
first_points, second_points = row
# Convert points from strings to integers
first_points = map(int, first_points.split(","))
second_points = map(int, second_points.split(","))
paired_points = zip(first_points, second_points)
curr_points = [Point(p[0], p[1]) \
for p in paired_points]
time_end = time.time()
print "total time: ", (time_end - time_start)

Currently, this takes nearly 7 seconds for 100,000 points, which seems very inefficient. Part of the inefficiency seems to stem from the calculation of
- and the conversion of these into objects.

Another part of the inefficiency seems to be the building up of
. Taking out the
line seems to make the code go from ~7 seconds to 2 seconds!

How can this be sped up? thanks.

FOLLOWUP Thanks for everyone's great suggestions - they were all helpful. but even with all the improvements, it's still about 3 seconds to process 100,000 entries. I'm not sure why in this case it's not just instant, and whether there's an alternative representation that would make it instant. Would coding this in Cython change things? Could someone offer an example of that? thanks again.

Answer Source

Simply running with pypy makes a big difference

$ python 
total time:  2.09194397926
$ pypy 
total time:  0.764246940613

disable gc didn't help for pypy

$ pypy 
total time:  0.763386964798

namedtuple for Point makes it worse

$ pypy 
total time:  0.888827085495

using itertools.imap, and itertools.izip

$ pypy 
total time:  0.615751981735

Using a memoized version of int and an iterator to avoid the zip

$ pypy 
total time:  0.423738002777 

Here is the code I finished with.

def test():
    import time
    def m_int(s, memo={}):
        if s in memo:
            return memo[s]
            retval = memo[s] = int(s)
            return retval
    data = get_data()
    all_point_sets = []
    time_start = time.time()
    for xs, ys in data:
        point_set = []
        # Convert points from strings to integers
        y_iter = iter(ys.split(","))
        curr_points = [Point(m_int(i), m_int(next(y_iter))) for i in xs.split(",")]
    time_end = time.time()
    print "total time: ", (time_end - time_start)
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