Need an advice

Nadav Horesh nadavh.horesh at gmail.com
Fri Dec 30 11:20:22 EST 2011


Remarks for the convolution subpackage:
1. The __init__.py should be probably changed to

from ext import pyconvolve as convolve

2. The test_convolution.py file is very instructive. It should be polished
a bit. I think it would be worthwhile to add also scipy.signal.sepfir2d
and cv2.sepFilter2D to the test.

3. I found the convolve speed in par with cv.convolve2d (it can be slower
or faster depending on the kernel)

   Nadav

2011/12/28 Nadav Horesh <nadavh.horesh at gmail.com>

> I compiled after setting the flags for a core2 linux machine.  A quick and
> dirty benchmark showed a x2 improvement over scipy.signal.sepfir2d.
> I think that are some declaration errors in the python code (for instance
> I think that the convolution __init__.py should be
>
> from ext import pyconvolve
>
> instead of
>
> from ext import convolve
>
>  I'll take a closer look later.
>
> Thank you,
>
>    Nadav.
>
>
>
> 2011/12/28 Tony Yu <tsyu80 at gmail.com>
>
>>
>>
>> On Tue, Dec 27, 2011 at 8:24 PM, Tony Yu <tsyu80 at gmail.com> wrote:
>>
>>>
>>>
>>> On Tue, Dec 27, 2011 at 8:29 AM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:
>>>
>>>> How can I get it?
>>>>
>>>>   Nadav
>>>>
>>>
>>> The code Stefan mentioned is in an old pull request (PR #16<https://github.com/scikits-image/scikits-image/pull/16>).
>>> That PR is from before the switch from scikits.image to skimage. I've made
>>> a new branch<https://github.com/tonysyu/scikits-image/commits/skimage-convolution>in my git repo with the convolution code in the new namespace.
>>>
>>> If you're already running skimage from git, then you can use git to
>>> clone this branch:
>>>
>>> git remote -f add tonysyu git at github.com:tonysyu/scikits-image.git
>>> git checkout -b convolution tonysyu/skimage-convolution
>>>
>>>
>>> In case this isn't familiar: The first line adds my git repo to your
>>> list of remotes, and the "-f" flag fetches the tags from my repo (this
>>> ensures that you have the info about my branches). My repo is now added to
>>> your repo as a remote with the name "tonysyu" (you can change this). The
>>> second line creates a new branch "convolution", clones my
>>> "skimage-convolution" branch into it, and checks it out.
>>>
>>> Hope that helps,
>>> -Tony
>>>
>>
>> Oops, I forgot to mention: I added a compile flag that is specific to my
>> system (In convolution/setup.py there's an include flag '-I/usr/...') that
>> should probably be removed. Also, I should mention that I haven't gotten
>> this branch to compile on my system (OSX). I believe it should compile OK
>> on Linux (after removing the '-I/usr/...' compile flag).
>>
>> Good luck,
>> -Tony
>>
>>>
>>> 2011/12/23 Stéfan van der Walt <stefan at sun.ac.za>
>>>
>>>> On Thu, Dec 22, 2011 at 10:44 PM, Nadav Horesh <nadavh.horesh at gmail.com>
>>>> wrote:
>>>> > The application is not too sophisticated, and I do use numpy, scipy
>>>> and
>>>> > skimage for all I need. The only problem is speed, I need the
>>>> processing to
>>>> > be at l5-10 time faster. Convolutions take most of the processing
>>>> time. I
>>>> > prefer a flexible solution that would speed up also common nonlinear
>>>> filters
>>>> > (i.e. a median filter).
>>>>
>>>> We have a PR in the pipeline for doing really, really fast
>>>> convolutions... but it needs a bit of work.  Would you like to have a
>>>> look at it?
>>>>
>>>> Stéfan
>>>>
>>>
>>
>>
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