Mailman 3 September 2009 - scikit-image

OpenCV?
by Mike Sarahan 02 Oct '09

02 Oct '09

Sorry if I missed this in discussions at the sprint, but is there any reason we're not taking advantage of OpenCV? It may be a little more than what this scikit is aiming to offer, but it has some really nice, well-optimized routines. It's BSD licensed. I have been using the ctypes-opencv python wrapper, which is also BSD licensed. Yes, it's another dependency, but it's really easy to get - Ubuntu & Fedora have packages, binaries are readily available for Windows, and it has built easily on my OSX system. If you guys think it's something worth including, I can work on getting the wrappers integrated with the scikit. -Mike

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Re: ideas for contributions
by Stéfan van der Walt 30 Sep '09

30 Sep '09

2009/9/25 Gary Ruben <gary.ruben(a)gmail.com>: > You may already know this, but pymorph is BSD licensed and may be a > good starting point for incorporating morphological functions: > http://luispedro.org/pymorph/ Damian has been working on morphological operators during the sprint, so I'll ask him to compare pymorph to the work he has done so far. It looks like pymorph pretty much covers all the Matlab functionality? > Also I have some small Finite Radon Transform routines, which are pure > Python and hence not super fast (but they are super fast compared to > Matlab) but they do work correctly. It's not a widely used transform > but if you're interested, I'm happy to contribute it to > scikits.image.transform. I'd be very interested to see this code included! Regards Stéfan

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Re: [SciPy-User] How to create multi-page tiff files with python tools?
by David Warde-Farley 30 Sep '09

30 Sep '09

On 29-Sep-09, at 2:24 PM, Ralf Gommers wrote: > On Tue, Sep 29, 2009 at 11:14 AM, Sebastian Haase > <seb.haase(a)gmail.com>wrote: > > Hi Sebastian, this is very useful functionality for me as well. > > The question I have is if your patched PIL includes fixes for 16-bit > images. > Right now I'm using a patched PIL kindly provided to me by Zachary > Pincus > that fixes 16-bit issues. I saw that some improvements for 16-bit were > included in PIL trunk but not his patches. Your patch is included it > seems, > so I could also run PIL trunk if someone can confirm that 16-bit TIF > images > work. I'd prefer Priithon though because then I could stop asking my > users > to compile PIL themselves... I've been following this discussion somewhat and I wanted to point out that (as far as I can remember) image I/O free of PIL dependence was one of the stated goals of the image scikit. I'm not sure much progress has been made on that front yet. It seems that common requirements not being met by PIL are a) full support for multipage TIFF (loading, creating, saving) b) 16-bit multipage TIFF Rather than monkeypatching PIL four ways from Sunday, maybe it would be best to direct efforts towards building a PIL-free alternative? Incorporation of very specific code from PIL shouldn't be an issue given that PIL is quite liberally licensed. David (P.S. I'm CCing the scikits-image list as well, should you want to join it, etc.)

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Re: ideas for contributions
by Mike Sarahan 25 Sep '09

25 Sep '09

Those radon transforms & filtered backprojection would be of great interest to me (I'm in electron microscopy.) I'd be interested in seeing those make it into the kit, and willing to help do any integration work. -Mike On Thu, Sep 24, 2009 at 9:01 PM, Gary Ruben <gary.ruben(a)gmail.com> wrote: > > You may already know this, but pymorph is BSD licensed and may be a > good starting point for incorporating morphological functions: > http://luispedro.org/pymorph/ > > Also, I'm going to advertise the existence of this toolbox around here > - I know a friend has some filtered back-projection code which may > still be based on numarray, but is apparently quite fast. I'll try to > get him to contribute it (and numpyify it first if necessary). > > Also I have some small Finite Radon Transform routines, which are pure > Python and hence not super fast (but they are super fast compared to > Matlab) but they do work correctly. It's not a widely used transform > but if you're interested, I'm happy to contribute it to > scikits.image.transform.

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ideas for contributions
by Gary Ruben 25 Sep '09

25 Sep '09

You may already know this, but pymorph is BSD licensed and may be a good starting point for incorporating morphological functions: http://luispedro.org/pymorph/ Also, I'm going to advertise the existence of this toolbox around here - I know a friend has some filtered back-projection code which may still be based on numarray, but is apparently quite fast. I'll try to get him to contribute it (and numpyify it first if necessary). Also I have some small Finite Radon Transform routines, which are pure Python and hence not super fast (but they are super fast compared to Matlab) but they do work correctly. It's not a widely used transform but if you're interested, I'm happy to contribute it to scikits.image.transform.

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ANN: Image Processing SciKit
by Stéfan van der Walt 25 Sep '09

25 Sep '09

Hi all, After a short sprint at SciPy 2009, we've put together the infrastructure for an Image Processing SciKit. The source code [1] and documentatin [2] is available online. WIth the infrastructure in place, the next focus will be on getting contributions (listed at [3]) merged. If you have code for generally useful image processing algorithms available, please consider contributing. Feel free to join further discussions on the scikit mailing list [4]. Kind regards Stéfan [1] http://github.com/stefanv/scikits.image [2] http://stefanv.github.com/scikits.image [3] http://conference.scipy.org/sprints [4] http://groups.google.com/group/scikits-image

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OpenImageIO
by Stéfan van der Walt 11 Sep '09

11 Sep '09

Hi all, The OpenImageIO project will soon have Python bindings available. If we are willing to introduce their library as a dependency, we'll be able to load many image formats. I'd be quite happy to stick to a pure Python loader as well, but I don't know if such code exists. http://openimageio.org/ Enjoy your weekend! Cheers Stéfan

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scikit-image September 2009