generic non-linear filtering that support selem and boundary handling

[Juan Nunez-Iglesias]

Stéfan, I thought I saw some message recently about access to some OSX
machines for scikit-image testing?

I have one (my laptop) but zero bandwidth for anything but the simplest
tests for now...

Juan.


On Tue, May 27, 2014 at 2:49 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:

> Basically OSX uses Clang, and Clang doesn't (yet) support OpenMP. Some
> people are working toward this, but it's not in there yet. OSX is the only
> architecture for which this is a problem.
>
> There are a lot of places in skimage where relatively simple optimizations
> (release the GIL, use prange) would reap very large performance benefits.
> I'd asked about this before, and it was viewed as not feasible due to
> Clang's limitations.
>
> However, I looked at this again just now and it *might *be that Cython
> simply ignores OpenMP features under Clang, compiling as if they didn't
> exist (i.e. basically substitution range for prange). If that is true, I
> could submit these without much issue... and we could expose pretty
> dramatic improvements to some existing Cython loops. Sadly, I don't have a
> Clang platform to test this behavior.
>
> Josh
>
>
> On Monday, May 26, 2014 10:48:15 PM UTC-5, Juan Nunez-Iglesias wrote:
>>
>> Josh, why the parallel stripping out? Is it a Cython version requirement?
>> We can always have this as a "dormant" PR for 1.0, for which we might bump
>> up the version required. It might also be possible to wrap the import
>> around a try-catch clause so that it fails gracefully on an earlier Cython
>> version.
>>
>> Juan.
>>
>>
>> On Tue, May 27, 2014 at 1:07 PM, Josh Warner <silvertrumpet999 at gmail.com>wrote:
>>
>>> Funny you should request this. I built a Cython framework do exactly
>>> what you want (arbitrary selem, boundary handling [padding], and even
>>> arbitrary weighting of the selem in 2D and 3D) for local *weighted *
>>> variance.
>>>
>>> The framework is about as useful as the actual calculation. Replace the
>>> innermost loop, change the name, and you get an entirely different
>>> non-linear weighted local feature. This requires a somewhat skilled user,
>>> but the framework is already done so it isn't as hard as it sounds.
>>>
>>> Trouble is, I used some features from cython.parallel so those would
>>> have to be stripped out, losing over an order of magnitude in speed. I've
>>> been kicking around submitting them, but going back and ripping out the
>>> parallel features is painful.
>>>
>>> If interested I can clean up and put them in a Gist or two.
>>>
>>> Josh
>>>
>>>
>>> On Monday, May 26, 2014 1:50:10 AM UTC-5, Chencan QIAN wrote:
>>>>
>>>> Essentially, this is something similar to scipy.ndimage.filters.generic_filter
>>>> (which is too slow because of its internal python for-loop), but
>>>> implemented in cython as with skimage.filter.rank family.
>>>>
>>>> Given the diversity within skimage.filter.rank, a generic function
>>>> would be very useful. For example, I'd like to calculate local variance,
>>>> which is conceptually similar to skimage.filter.rank.mean, but not
>>>> supported currently.
>>>>
>>>> I guess the absence of such a function must be due to some unresolved
>>>> technical obstacle?
>>>>
>>>> Thanks~
>>>>
>>>> Chencan
>>>>
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