[SciPy-user] ndimage zero-ignorant filters, or other ways to fill holes

Carlos da Silva Santos carlos.s.santos@gmail....
Wed Nov 26 13:34:38 CST 2008

On Tue, Nov 25, 2008 at 7:13 AM, Sebastian Haase <haase@msg.ucsf.edu> wrote:
> On Mon, Nov 24, 2008 at 10:48 PM, Carlos da Silva Santos
> <carlos.s.santos@gmail.com> wrote:
>> On Mon, Nov 24, 2008 at 1:03 PM, Vincent Schut <schut@sarvision.nl> wrote:
>>> If someone comes up with another brillant idea to fill the zero-gaps in
>>> my images with values that are in reasonable range of the gap's
>>> surroundings, I'd also be very grateful. Keep in mind that the images
>>> typically are pretty large, though. 7000x7000 pixels is no exception.
>> Maybe you could use ndimage.morphology.grey_closing, I cant find a
>> code example using it, but the idea is similar to the examples
>> featured in this page:
>> http://www.mmorph.com/pymorph/morph/morph/mmclose.html
>> The "close hole" operator is probably closer to what you intended:
>> http://www.mmorph.com/pymorph/morph/morph/mmclohole.html
>> I am not sure whether this operator is implemented in the free version
>> of pymorph, maybe you should give it a try:
>> http://luispedro.org/pymorph
>> Hope this helps.

Hi Sebastian,

> Hi  Carlos,
> the links you provided look very interesting !

Morphology is a quite nice tool, indeed.

> Would you be able to answer some further questions ?
> e.g.
> the original pymorph (http://www.mmorph.com/pymorph) appears to have a
> BSD license, did this change for the
> luispedro.org pymorph ?

According to Luis Pedro, the license is the same:

"The license stays BSD..."

> Is pymorph all 2D (only) ?
> What data data-types does pymorph support ? float32 ?

Actually, I never used pymorph. But quoting from the docs:

"The Morphology Toolbox mainly supports four types of images according
to their pixel datatypes : binary, unsigned gray scale uint8 and
uint16, and signed gray scale int32. Most functions work for 1D, 2D
and 3D images."

I believe the morphological operators available in ndimage.morphology
work with floating point, can anyone confirm this? But pymorph has
much more operators than ndimage.morphology.

In my experience, it is not that common to use floating point images
in applications involving morphology. Do you have anything specific in

Hope this helps,


> Thanks,
> Sebastian Haase
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