[Numpy-discussion] neighborhood iterator
Zachary Pincus
zachary.pincus at yale.edu
Mon Nov 23 15:25:12 EST 2009
Hi,
Having just written some cython code to iterate a neighborhood across
an array, I have some ideas about features that would be useful for a
general frame. Specifically, being able to pass in a "footprint"
boolean array to define the neighborhood is really useful in many
contexts. Also useful is the ability to query the offset of the
current pixel from the center of the neighborhood. (These two
features, plus very efficient handling of boundary conditions by
breaking the image into regions where the conditions are and are not
required, make the image iterators in ITK really nice to use.)
Zach
On Nov 23, 2009, at 9:12 AM, Nadav Horesh wrote:
>
> Thank you, this is a start. I seems that there are more issues to
> resolve. I am trying to make a general frame that would enable one
> to write filters using this iterator.
>
>
> Nadav
>
> -----Original Message-----
> From: numpy-discussion-bounces at scipy.org on behalf of David Warde-
> Farley
> Sent: Mon 23-Nov-09 03:21
> To: Discussion of Numerical Python
> Subject: Re: [Numpy-discussion] neighborhood iterator
>
>
> On 22-Nov-09, at 12:50 PM, Nadav Horesh wrote:
>
>>
>> I wonder if the neighbourhood iterator can be used as a more
>> efficient replacement for ndimage.generic_filter. Is there a way to
>> use it from cython?
>
> Yes, using the NumPy C API, called like any other C function is from
> Cython. Something like:
>
> ######################
>
> import numpy as np
> cimport numpy as np
>
> cdef extern from "numpy/arrayobject.h":
> object PyArray_NeighborhoodIterNew(object iter, np.npy_intp
> bounds,
> int mode, object, np.ndarray
> fill_value)
> int PyArrayNeighborhoodIter_Next(object iter)
> int PyArrayNeighborhoodIter_Reset(object iter)
>
> ######################
>
> should do the trick.
>
> Note that you'll need to call np.import_array() before using any of
> these functions to initialize the C API, I think.
>
> David
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