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@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@gmail.com>

...

On Tue, Dec 27, 2011 at 8:24 PM, Tony Yu <tsyu80@gmail.com> wrote:

...

On Tue, Dec 27, 2011 at 8:29 AM, Nadav Horesh <nadavh.horesh@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@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@sun.ac.za>

...

...

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

On Thu, Dec 22, 2011 at 10:44 PM, Nadav Horesh <nadavh.horesh@gmail.com> wrote: 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