Need an advice

[Tony Yu]

On Fri, Dec 30, 2011 at 8:20 AM, Nadav Horesh <nadavh.horesh at gmail.com>wrote:

> Remarks for the convolution subpackage:
> 1. The __init__.py should be probably changed to
>
> from ext import pyconvolve as convolve
>

Agreed. Alternatively, the c-method could be renamed so that the python
method in ext can be named 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
>

Thanks for testing the code.

I've got the code compiling on my system now, so I was able to clean up a
few things. Could you update to what's currently on my skimage-convolution
branch to check that it builds on your system? If not, what flags do you
have to change/add to get it to compile?

-Tony

P.S. If any one else is building this on OS X: ppc compatible builds is
turned on by default (at least on my system). This should be turned off
before building. Add the following line to ~/.profile, or just run it right
before building:

export ARCH_FLAGS="-arch i386 -arch x86_64"




>
> 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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