optimization pointers?

[r.e.s.]

Would anyone care to offer pointers on how the following code
might be optimized? Or alternatives? ...

---
def lz(string):
""" Return the Lempel-Ziv complexity (LZ78) of string. """

vocabulary = []
word = ''
for char in string:
word += char
if word not in vocabulary:
vocabulary.appe nd(word)
word = ''
return len(vocabulary)
---

On my 2 GHz system running PythonWin, the above code averages
about 1.3 hrs to process a 1 MB string. I'd hoped to compute
LZ78 for multi-GB files, but it seems infeasible. (?)

Thanks for any feedback.
--
r.e.s.

[Mel Wilson]

Re: optimization pointers?

In article <Bz5Cb.7881$_r6 .5116@newsread1 .news.pas.earth link.net>,
"r.e.s." <r.s@XXmindspri ng.com> wrote:[color=blue]
>Would anyone care to offer pointers on how the following code
>might be optimized? Or alternatives? ...
>
>---
>def lz(string):
> """ Return the Lempel-Ziv complexity (LZ78) of string. """
>
> vocabulary = []
> word = ''
> for char in string:
> word += char
> if word not in vocabulary:
> vocabulary.appe nd(word)
> word = ''
> return len(vocabulary)
>---
>
>On my 2 GHz system running PythonWin, the above code averages
>about 1.3 hrs to process a 1 MB string. I'd hoped to compute
>LZ78 for multi-GB files, but it seems infeasible. (?)[/color]

One simple improvement is to get rid of

if an_item not in a_list

which does a linear search over the list. A dictionary is faster.

Without a full benchmark, it seems that appending


def lz_complexity (s):
voc = {}
word = ''
for c in s:
word += c
if not voc.get (word, False):
voc[word] = True
word = ''
return len (voc.keys())

if __name__ == '__main__':
import time
text = file ('lzc.py', 'rt').read()
t0 = time.clock()
t0 = time.clock() - t0

c = lz (text)
t1 = time.clock()
c = lz (text)
t1 = time.clock() - t1

c = lz_complexity (text)
t2 = time.clock()
c = lz_complexity (text)
t2 = time.clock() - t2

print 'T1:', t1 - t0
print 'T2:', t2 - t0


will show about a x6 speedup.

Avoiding

a_string += another_string

is a traditional speedup, but it seems you'll be needing the
string form for every character processed, so it may not buy
much in this case.

Regards. Mel.

[Anton Vredegoor]

Re: optimization pointers?

"r.e.s." <r.s@XXmindspri ng.com> wrote:
[color=blue]
>Would anyone care to offer pointers on how the following code
>might be optimized? Or alternatives? ...
>
>---
>def lz(string):
> """ Return the Lempel-Ziv complexity (LZ78) of string. """
>
> vocabulary = []
> word = ''
> for char in string:
> word += char
> if word not in vocabulary:
> vocabulary.appe nd(word)
> word = ''
> return len(vocabulary)
>---
>
>On my 2 GHz system running PythonWin, the above code averages
>about 1.3 hrs to process a 1 MB string. I'd hoped to compute
>LZ78 for multi-GB files, but it seems infeasible. (?)[/color]

On a 300 mhz celeron the script below takes about ten or twenty
seconds, the original lz is commented out as it never seems to finish
for longer strings.

Anton

p.s. the file I used is here:

http://sailor.gutenberg.org/etext97/1donq10.zip

import sets

def lz(string):
""" Return the Lempel-Ziv complexity (LZ78) of string. """

vocabulary = []
word = ''
for char in string:
word += char
if word not in vocabulary:
vocabulary.appe nd(word)
word = ''
return len(vocabulary)

def lzx(string):
""" Return the Lempel-Ziv complexity (LZ78) of string. """

vocabulary = sets.Set()
word = ''
for char in string:
word += char
if word not in vocabulary:
vocabulary.add( word)
word = ''
return len(vocabulary)

def test():
fn = '1donq10.txt'
s = file(fn,'rb').r ead(1000000)
print lzx(s)
#print lz(s)


if __name__=='__ma in__':
test()

[r.e.s.]

Re: optimization pointers?

"Mel Wilson" <mwilson@the-wire.com> wrote ...
[color=blue]
> One simple improvement is to get rid of
>
> if an_item not in a_list
>
> which does a linear search over the list.
> A dictionary is faster.
>
> Without a full benchmark, it seems that[/color]
[...][color=blue]
> will show about a x6 speedup.[/color]

I really appreciate the suggestions -- both yours
and Anton's.

After making the changes you indicated, the code
runs in about 1/500th the time of the original
(i.e. about 2 sec per MB for strings in RAM). The
sets idea also speeds things up tremendously, but
not as much -- it takes about 70% longer than the
dictionary approach.

Thanks again.
--
r.e.s.

[Anthony McDonald]

Re: optimization pointers?

"Mel Wilson" <mwilson@the-wire.com> wrote in message
news:rzO2/ks/KXcX089yn@the-wire.com...[color=blue]
>
> One simple improvement is to get rid of
>
> if an_item not in a_list
>
> which does a linear search over the list. A dictionary is faster.
>
> Without a full benchmark, it seems that appending
>
>
> def lz_complexity (s):
> voc = {}
> word = ''
> for c in s:
> word += c
> if not voc.get (word, False):
> voc[word] = True
> word = ''
> return len (voc.keys())
>
> if __name__ == '__main__':
> import time
> text = file ('lzc.py', 'rt').read()
> t0 = time.clock()
> t0 = time.clock() - t0
>
> c = lz (text)
> t1 = time.clock()
> c = lz (text)
> t1 = time.clock() - t1
>
> c = lz_complexity (text)
> t2 = time.clock()
> c = lz_complexity (text)
> t2 = time.clock() - t2
>
> print 'T1:', t1 - t0
> print 'T2:', t2 - t0
>
>
> will show about a x6 speedup.
>
> Avoiding
>
> a_string += another_string
>
> is a traditional speedup, but it seems you'll be needing the
> string form for every character processed, so it may not buy
> much in this case.
>
> Regards. Mel.[/color]

Heres my contribution, removing the string append in favour of slices. Buys
a little speed thanks to xrange.

def lz_comp_mine(te xt):
voc = {}
st = 0
for cur in xrange(1,len(te xt)+1):
if not voc.get(text[st:cur], False):
voc[text[st:cur]] = True
st = cur
return len(voc)

Anthony McDonald

[Mel Wilson]

Re: optimization pointers?

In article <3fd9cdf1$0$697 0$7a628cd7@news .club-internet.fr>,
"Anthony McDonald" <tonym1972(at)c lub-internet(in)fr> wrote:[color=blue]
>Heres my contribution, removing the string append in favour of slices. Buys
>a little speed thanks to xrange.
>
>def lz_comp_mine(te xt):
> voc = {}
> st = 0
> for cur in xrange(1,len(te xt)+1):
> if not voc.get(text[st:cur], False):
> voc[text[st:cur]] = True
> st = cur
> return len(voc)[/color]

Nice touch! I tried slices and took a huge performance
hit (almost 3x the list version) but I didn't use `for ... in
xrange ...`. It must have all been in the while-loop test
and index incrementing.

Regards. Mel.

[Anthony McDonald]

Re: optimization pointers?

"Mel Wilson" <mwilson@the-wire.com> wrote in message
news:xIf2/ks/Kvyd089yn@the-wire.com...[color=blue]
>
> Nice touch! I tried slices and took a huge performance
> hit (almost 3x the list version) but I didn't use `for ... in
> xrange ...`. It must have all been in the while-loop test
> and index incrementing.
>
> Regards. Mel.[/color]

Thanks.

My original attempt which incidentally used range was about half a second
slower than yours with 700K of test data. Just as I was about to close the
editor window I noticed your return statement.

return len (voc.keys())

Which creates a list of keys to then apply len to, but thats an unneeded
step as len applied directly to a dictionary returns the number of keys. I
made the change and gained 7 hundreds of a second. Not much, still behind
yours, but it suggested that chainging range to xrange and avoiding the list
creation might help. Viola!

The interesting thing that benchmarking with test data shows, is that the
difference in speed between our 2 routines is about 0.05secs per 700K
processed. That difference remains constant at least upto 80Mb of input
data, implying that slices are no more efficent than string appending, and
may actually in this case be less efficent.

Anthony McDonald

[Anton Vredegoor]

Re: optimization pointers?

"Anthony McDonald" <tonym1972(at)c lub-internet(in)fr> wrote:
[color=blue]
>return len (voc.keys())
>
>Which creates a list of keys to then apply len to, but thats an unneeded
>step as len applied directly to a dictionary returns the number of keys.[/color]

Below are two more small optimization possibilities. Originally I
wasn't going to post them because they are way into micro optimization
country and because the setdefault solution is beautiful but blond. At
least on some of my machines however they are both faster than the
solutions offered so far.

Anton

def lzx(s):
word,D = '',{}
Dget, Dset = D.get, D.__setitem__
for c in s:
word += c
if not Dget(word):
Dset(word,True)
word = ''
return len(D)

def lzy(s):
j,D = 0,{}
func = D.setdefault
for i in xrange(1,len(s) +1):
if func(s[j:i],j) is j: j = i
return len(D)