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From: Kyp on 31 Jan 2010 19:22
On Jan 31, 1:06 pm, John Bokma <j...(a)castleamber.com> wrote:
> Kyp <k...(a)stsci.edu> writes:
> > Is there a way to get the first X # of files from a dir with lots of
> > files, that does not take a long time to run?
>
> Assuming Linux: what does time
>
>  ls thedir | head
>
> give?
>
> with thedir the name of the actual dir
about 3 seconds.

3.086u 0.201s 0:03.32 98.7% 0+0k 0+0io 0pf+0w

>
> Also how many is many files?
over 100K (I know I should not do that, but it's a temp dir holding
files to be transferred)
thanx, mark



From: Kyp on 31 Jan 2010 19:23
On Jan 31, 2:44 pm, Peter Otten <__pete...(a)web.de> wrote:
> Kyp wrote:
> > I have a dir with a large # of files that I need to perform operations
> > on, but only needing to access a subset of the files, i.e. the first
> > 100 files.
>
> > Using glob is very slow, so I ran across iglob, which returns an
> > iterator, which seemed just like what I wanted. I could iterate over
> > the files that I wanted, not having to read the entire dir.
>
> > So the iglob was faster, but accessing the first file took about the
> > same time as glob.glob.
>
> > Here's some code to compare glob vs. iglob performance,  it outputs
> > the time before/after a glob.iglob('*.*') files.next() sequence and a
> > glob.glob('*.*') sequence.
>
> > #!/usr/bin/env python
>
> > import glob,time
> > print '\nTest of glob.iglob'
> > print 'before       iglob:', time.asctime()
> > files = glob.iglob('*.*')
> > print 'after        iglob:',time.asctime()
> > print files.next()
> > print 'after files.next():', time.asctime()
>
> > print '\nTest of glob.glob'
> > print 'before        glob:', time.asctime()
> > files = glob.glob('*.*')
> > print 'after         glob:',time.asctime()
>
> > Here are the results:
>
> > Test of glob.iglob
> > before       iglob: Sun Jan 31 11:09:08 2010
> > after        iglob: Sun Jan 31 11:09:08 2010
> > foo.bar
> > after files.next(): Sun Jan 31 11:09:59 2010
>
> > Test of glob.glob
> > before        glob: Sun Jan 31 11:09:59 2010
> > after         glob: Sun Jan 31 11:10:51 2010
>
> > The results are about the same for the 2 approaches, both took about
> > 51 seconds. Am I doing something wrong with iglob?
>
> No, but iglob() being lazy is pointless in your case because it uses
> os.listdir() and fnmatch.filter() underneath which both read the whole
> directory before returning anything.
>
> > Is there a way to get the first X # of files from a dir with lots of
> > files, that does not take a long time to run?
>
> Here's my attempt. It turned out to be more work than expected, so I cut a
> few corners. It's Linux-only "works on my machine" code, but may give you
> some hints on how to proceed.
>
> from ctypes import *
> import fnmatch
> import glob
> import os
> import re
> from itertools import ifilter, imap
>
> class dirent(Structure):
>     "works on my machine ;)"
>     _fields_ = [
>         ("d_ino", c_long),
>         ("d_off", c_long),
>         ("d_reclen", c_ushort),
>         ("d_type", c_ubyte),
>         ("d_name", c_char*256)]
>
> direntp = POINTER(dirent)
>
> LIBC = "libc.so.6"
> cdll.LoadLibrary(LIBC)
> libc = CDLL(LIBC)
> libc.readdir.restype = direntp
>
> def diriter(dir):
>     "lazy partial replacement for os.listdir()"
>     # errors? what errors?
>     dirp = libc.opendir(dir)
>     if not dirp:
>         return
>     try:
>         while True:
>             ep = libc.readdir(dirp)
>             if not ep:
>                 break
>             yield ep.contents.d_name
>     finally:
>         libc.closedir(dirp)
>
> def filter(names, pattern):
>     "lazy partial replacement for fnmatch.filter()"
>     import posixpath
>
>     pattern = os.path.normcase(pattern)
>     r = fnmatch.translate(pattern)
>     r = re.compile(r)
>
>     if os.path is not posixpath:
>         names = imap(os.path.normcase, names)
>
>     return ifilter(r.match, names)
>
> def globiter(path):
>     "lazy partial replacement for glob.glob()"
>     dir, filename = os.path.split(path)
>     if glob.has_magic(dir):
>         raise ValueError("wildcards in directory not supported")
>     return filter(diriter(dir), filename)
>
> if __name__ == "__main__":
>     import sys
>     [pattern] = sys.argv[1:]
>     for name in globiter(pattern):
>         print name
>
> Peter

I'll give it a try, thanx for the reply.
mark
From: Cameron Simpson on 14 Feb 2010 01:12
On 31Jan2010 16:23, Kyp <kyp(a)stsci.edu> wrote:
| On Jan 31, 2:44 pm, Peter Otten <__pete...(a)web.de> wrote:
| > Kyp wrote:
| > > I have a dir with a large # of files that I need to perform operations
| > > on, but only needing to access a subset of the files, i.e. the first
| > > 100 files.
| > > Using glob is very slow, so I ran across iglob, which returns an
| > > iterator, which seemed just like what I wanted. I could iterate over
| > > the files that I wanted, not having to read the entire dir.
[...]
| > > So the iglob was faster, but accessing the first file took about the
| > > same time as glob.glob.
| >
| > > Here's some code to compare glob vs. iglob performance,  it outputs
| > > the time before/after a glob.iglob('*.*') files.next() sequence and a
| > > glob.glob('*.*') sequence.
| >
| > > #!/usr/bin/env python
| >
| > > import glob,time
| > > print '\nTest of glob.iglob'
| > > print 'before       iglob:', time.asctime()
| > > files = glob.iglob('*.*')
| > > print 'after        iglob:',time.asctime()
| > > print files.next()
| > > print 'after files.next():', time.asctime()
| >
| > > print '\nTest of glob.glob'
| > > print 'before        glob:', time.asctime()
| > > files = glob.glob('*.*')
| > > print 'after         glob:',time.asctime()
| >
| > > Here are the results:
| >
| > > Test of glob.iglob
| > > before       iglob: Sun Jan 31 11:09:08 2010
| > > after        iglob: Sun Jan 31 11:09:08 2010
| > > foo.bar
| > > after files.next(): Sun Jan 31 11:09:59 2010
| >
| > > Test of glob.glob
| > > before        glob: Sun Jan 31 11:09:59 2010
| > > after         glob: Sun Jan 31 11:10:51 2010
| >
| > > The results are about the same for the 2 approaches, both took about
| > > 51 seconds. Am I doing something wrong with iglob?
| >
| > No, but iglob() being lazy is pointless in your case because it uses
| > os.listdir() and fnmatch.filter() underneath which both read the whole
| > directory before returning anything.
| >
| > > Is there a way to get the first X # of files from a dir with lots of
| > > files, that does not take a long time to run?
| >
| > Here's my attempt. [...open directory and read native format...]

I'd be inclined first to time os.listdir('.') versus glob.lgo('*.*').

Glob routines tend to lstat() every matching name to ensure the path
exists. That's very slow. If you just do os.listdir() and choose your
100 nmaes, you only need to stat (or just try to open) them.

So time glob.glob("*.*") versus os.listdir(".") first.

Generally, with a large directory, stat time will change performance
immensely.
--
Cameron Simpson <cs(a)zip.com.au> DoD#743
http://www.cskk.ezoshosting.com/cs/

Usenet is essentially a HUGE group of people passing notes in class. --R. Kadel
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