[Numpy-discussion] Efficient numpy slicing for a "sliding window approach".

josef.pktd@gmai... josef.pktd@gmai...
Fri Feb 20 23:56:48 CST 2009


On Sat, Feb 21, 2009 at 12:36 AM, Nicolas Pinto <pinto@mit.edu> wrote:
> Thanks a lot for the pointer to segmentaxis. I'm trying to use it "as is"
> and it seems that I need to a big reshape before the matrix multiplication.
> Am I missing something ?
>
>
> ========================================
>
> import numpy as np
> from numpy import dot, transpose
>
> arrh, arrw, arrd = 480,640,96
> arr = np.random.randn(arrh, arrw, arrd).astype("float32")
>
> stride = 16
> winh, winw, wind = 128,64,96
>
> limit = 100
>
> clas_w = np.random.randn(8,4,96).astype("float32").ravel()
>
> from segmentaxis import segment_axis
>
> nh, nw = arrh-winh+1, arrw-winw+1
>
> @profile
> def func_loop(arr):
>
>     resps = np.empty((nh,nw), dtype="float32")
>     for j in xrange(nh):
>          for i in xrange(nw):
>             win = arr[j:j+winh:stride, i:i+winw:stride]
>             win = win.ravel()
>             resp = dot(win, clas_w)
>             resps[j,i] = resp
>
>     resps = resps.ravel()
>     print resps.mean()
>
>
> @profile
> def func_segment(arr):
>
>     arr = segment_axis(arr, winh, winh-1, axis=0)
>     arr = arr[:, ::stride]
>
>     arr = segment_axis(arr, winw, winw-1, axis=2)
>     arr = arr[:, :, :, ::stride]
>
>     arr = transpose(arr, [0, 2, 1, 3, 4])
>     arr = arr.reshape(-1, clas_w.size)
>
>     resps2 = dot(arr, clas_w)
>
>     resps2 = resps2.ravel()
>     print resps2.mean()
>
>     # ...
>
> func_loop(arr)
>
> func_segment(arr)
>
>
> ========================================
>
>
> % python kernprof.py -l -v sliding_win_all.py
> w-0.0500485824034
> segmentaxis.py:94: UserWarning: Problem with ndarray creation forces copy.
>   warnings.warn("Problem with ndarray creation forces copy.")
> -0.0500485824034
> Wrote profile results to sliding_win_all.py.lprof
> Timer unit: 1e-06 s
>
> File: sliding_win_all.py
> Function: func_loop at line 18
> Total time: 3.9785 s
>
> Line #      Hits         Time  Per Hit   % Time  Line Contents
> ==============================================================
>     18                                           @profile
>     19                                           def func_loop(arr):
>     20
>     21         1           28     28.0      0.0      resps =
> np.empty((nh,nw), dtype="float32")
>     22       354          308      0.9      0.0      for j in xrange(nh):
>     23    204034       199753      1.0      5.0           for i in
> xrange(nw):
>     24    203681       691915      3.4     17.4              win =
> arr[j:j+winh:stride, i:i+winw:stride]
>     25    203681      1341174      6.6     33.7              win =
> win.ravel()
>     26    203681      1417998      7.0     35.6              resp = dot(win,
> clas_w)
>     27    203681       326520      1.6      8.2              resps[j,i] =
> resp
>     28
>     29         1            2      2.0      0.0      resps = resps.ravel()
>     30         1          805    805.0      0.0      print resps.mean()
>
> File: sliding_win_all.py
> Function: func_segment at line 33
> Total time: 3.82026 s
>
> Line #      Hits         Time  Per Hit   % Time  Line Contents
> ==============================================================
>     33                                           @profile
>     34                                           def func_segment(arr):
>     35
>     36         1           43     43.0      0.0      arr = segment_axis(arr,
> winh, winh-1, axis=0)
>     37         1            4      4.0      0.0      arr = arr[:, ::stride]
>     38
>     39         1       546505 546505.0     14.3      arr = segment_axis(arr,
> winw, winw-1, axis=2)
>     40         1           12     12.0      0.0      arr = arr[:, :, :,
> ::stride]
>     41
>     42         1           12     12.0      0.0      arr = transpose(arr,
> [0, 2, 1, 3, 4])
>     43         1      2435047 2435047.0     63.7      arr = arr.reshape(-1,
> clas_w.size)
>     44
>     45         1       837700 837700.0     21.9      resps2 = dot(arr,
> clas_w)
>     46
>     47         1           41     41.0      0.0      resps2 = resps2.ravel()
>     48         1          892    892.0      0.0      print resps2.mean()
>
>
> On Fri, Feb 20, 2009 at 11:55 PM, David Cournapeau <cournape@gmail.com>
> wrote:
>>
>> On Sat, Feb 21, 2009 at 1:46 PM, Nicolas Pinto <pinto@mit.edu> wrote:
>> > Dear all,
>> >
>> > I'm trying to optimize the code below and I was wondering if there is an
>> > efficient method that could reduce the numpy slicing overheard without
>> > going
>> > with cython. Is there anyway I could use mgrid to get a matrix with all
>> > my
>> > "windows" and then do a large matrix multiply instead?
>>
>> If you only care about removing the two loops for the per-window
>> processing, Anne Archibald and Robert Kern wrote a very useful
>> function, segment_axis, which is like the matlab buffer function on
>> steroids, using numpy stride tricks (to avoid copies in many cases). I
>> think that would do everything you want, right ? I use it a lot in my
>> own code, it may be worth being included in numpy or scipy proper.
>>
>>
>> http://projects.scipy.org/scipy/scikits/browser/trunk/talkbox/scikits/talkbox/tools/segmentaxis.py
>>
>> David
>> _______________________________________________
>> Numpy-discussion mailing list
>> Numpy-discussion@scipy.org
>> http://projects.scipy.org/mailman/listinfo/numpy-discussion
>
>
> Thanks again!
>
> --
> Nicolas Pinto
> Ph.D. Candidate, Brain & Computer Sciences
> Massachusetts Institute of Technology, USA
> http://web.mit.edu/pinto
>
> _______________________________________________
> Numpy-discussion mailing list
> Numpy-discussion@scipy.org
> http://projects.scipy.org/mailman/listinfo/numpy-discussion
>
>

Hi,

I don't really understand your array dimension, but to me it seems
that you could use ndimage.correlate2d for this.

Josef


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