scikit-image October 2011

scikit-image@python.org

12 participants
89 discussions

Re: A big thanks for 0.3!
by Emmanuelle Gouillart 10 Oct '11

10 Oct '11

A big thanks to you, StÃ¯Â¿Â½fan, for all your work and the energy that you devoted to this release! As you say, let's keep up the good work, move quickly to skimage, write a lot of documentation, and users and developers will come naturally. Cheers, Emmanuelle On Mon, Oct 10, 2011 at 04:08:42AM -0700, StÃ¯Â¿Â½fan van der Walt wrote: > Hi all, > To everyone who contributed to the 0.3 release, a big word of thanks! > We've hit a turning point: more and more people ask about the project, > notice the work that's being done, and--most importantly--use it. > This could not have happened without your valuable contributions. > We've gathered some good momentum; let's keep the ball rolling and > release 0.4 within the next few weeks, after doing the rename to > `skimage`. There's also a lot of room for new narrative > documentation, although the examples gallery is already a wonderful > addition (thanks Emmanuelle and scikit-learn!): > http://scikits-image.org/docs/dev/auto_examples/ > Keep up the good work! > StÃ¯Â¿Â½fan

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A big thanks for 0.3!
by Stéfan van der Walt 10 Oct '11

10 Oct '11

Hi all, To everyone who contributed to the 0.3 release, a big word of thanks! We've hit a turning point: more and more people ask about the project, notice the work that's being done, and--most importantly--use it. This could not have happened without your valuable contributions. We've gathered some good momentum; let's keep the ball rolling and release 0.4 within the next few weeks, after doing the rename to `skimage`. There's also a lot of room for new narrative documentation, although the examples gallery is already a wonderful addition (thanks Emmanuelle and scikit-learn!): http://scikits-image.org/docs/dev/auto_examples/ Keep up the good work! Stéfan

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scikits-image 0.3 release
by Stéfan van der Walt 10 Oct '11

10 Oct '11

Announcement: scikits.image 0.3 =============================== After a brief (!) absence, we're back with a new and shiny version of scikits.image, the image processing toolbox for SciPy. This release runs under all major operating systems where Python (>=2.6 or 3.x), NumPy and SciPy can be installed. For more information, visit our website http://scikits-image.org or the examples gallery at http://scikits-image.org/docs/0.3/auto_examples/ New Features ------------ - Shortest paths - Total variation denoising - Hough and probabilistic Hough transforms - Radon transform with reconstruction - Histogram of gradients - Morphology, including watershed, connected components - Faster homography transformations (rotations, zoom, etc.) - Image dtype conversion routines - Line drawing - Better image collection handling - Constant time median filter - Edge detection (canny, sobel, etc.) - IO: Freeimage, FITS, Qt and other image loaders; video support. - SIFT feature loader - Example data-sets ... as well as many bug fixes and minor updates. Contributors for this release ----------------------------- Martin Bergtholdt Luis Pedro Coelho Chris Colbert Damian Eads Dan Farmer Emmanuelle Gouillart Brian Holt Pieter Holtzhausen Thouis (Ray) Jones Lee Kamentsky Almar Klein Kyle Mandli Andreas Mueller Neil Muller Zachary Pincus James Turner Stefan van der Walt Gael Varoquaux Tony Yu

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Re: releasing & packaging vs. renaming
by Emmanuelle Gouillart 10 Oct '11

10 Oct '11

> I propose that we make the 0.3 release today as planned, and then work > in the coming week to bring out 0.4 with the rename. 0.4 will then be > the first version in Debian. Sounds great!

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interpolation issue...
by Jérôme Kieffer 10 Oct '11

10 Oct '11

Hi all, This is my first post on this list, but I think I met most participant at EuroScipy this summer. I write code for scientists and it seams to be a common problem to do "interpolation with given constrains" (in tomography, but also in other fields like [1]). A common case is the polar transformation: x,y -> r,theta Usually one takes a destination space coordinate (r,theta), look for input coordinates (x,y) and interpolate the neighbours with bilinear or bicubic spline. It is a backwards interpolation and plenty of implementations are available. First constraint: all signal in input has to appear in output: interpolation has to be done in "forwards" mode and can be done with 2D histogramming. Thanks to cython it is even 10x faster than the numpy implementation (0.5s for 4Mpix float64). Second constraint is that I need to conserve the surface density in the transformation. One idea is to cut pixels (4 corners) into triangles (2 minimum), the number of them varying with the spatial extension of the pixel in destination space (4 triangle if 1 bin boundary, 6 if 2 bin boundaries, ....) ... then do the histogramming as before but the cost is likely to be huge. Beside this I am convinced to re-invent the wheel ... even if I was unable to find anything in google but I am probably lacking the good keyword. Do you know this problem and what implementations already exists ?? Thanks for reading this "long email" -- Jérôme Kieffer <jerome.kieffer(a)terre-adelie.org> [1]: https://forge.epn-campus.eu/attachments/1459/20111010-PyFAI-Poster-A0.pdf

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Re: releasing & packaging vs. renaming
by Tony Yu 09 Oct '11

09 Oct '11

2011/10/9 Stéfan van der Walt <stefan(a)sun.ac.za> > On Sun, Oct 9, 2011 at 2:02 PM, Emmanuelle Gouillart > <emmanuelle.gouillart(a)nsup.org> wrote: > > > >> If we start putting more interfaces to code in the top level module > (right > >> now, only functions from `util` are there) or automatically importing > >> submodules (e.g. `io` would be a good candidate), then > adopting/promoting > >> the convention "import skimage as ski" would be nice (so the one > import > >> would give me `ski.img_as_float` and `ski.io.imread`). > > > > + 1 > > I propose that we make the 0.3 release today as planned, and then work > in the coming week to bring out 0.4 with the rename. 0.4 will then be > the first version in Debian. release early, release often: +1

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Re: releasing & packaging vs. renaming
by Emmanuelle Gouillart 09 Oct '11

09 Oct '11

> If we start putting more interfaces to code in the top level module (right > now, only functions from `util` are there) or automatically importing > submodules (e.g. `io` would be a good candidate), then adopting/promoting > the convention "import skimage as ski" would be nice (so the one import > would give me `ski.img_as_float` and `ski.io.imread`). + 1

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Re: releasing & packaging vs. renaming
by Andreas Mueller 09 Oct '11

09 Oct '11

On 10/09/2011 11:40 AM, StÃ¯Â¿Â½fan van der Walt wrote: > On Sun, Oct 9, 2011 at 2:08 AM, Nelle Varoquaux > <nelle.varoquaux(a)gmail.com> wrote: >> 2011/10/9 StÃ¯Â¿Â½fan van der Walt<stefan(a)sun.ac.za> >>> 2011/10/8 StÃ¯Â¿Â½fan van der Walt<stefan(a)sun.ac.za>: >>>> On Sat, Oct 8, 2011 at 9:34 PM, Tony Yu<tsyu80(a)gmail.com> wrote: >>>>> Agreed: there's definitely a wide range of activity among the scikits. >>>>> sklearn and statsmodels are probably a couple of the more active ones, >>>>> so >>>>> they'd be good examples to follow. And I also agree that changing the >>>>> name >>>>> sooner, rather than later, would be best. +1 >>>> Is there a preference between `skimage` and `skimg` ? >>> Actually, `ski` is also available. Three letters--not too hard to >>> type, doesn't sound awful (es-kay-eye for scikits image), and after >>> all--it's just a module name :) >> I don't whether you'd take this in account, but it's quite hard to google. >> Googling sklearn directly links to the scikit-learn documentation. >> Same with statsmodels. > Thanks, that's a valid concern. Seems like skimage is the top vote so > far, then. Any other votes? > Don't know if this is a good argument but people might rather be googleing "python ski", which is easy to google. For this reason I am ambivalent between ski and skimage. Cheers, Andy

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Challenge: Speed up seam carving example
by Stéfan van der Walt 09 Oct '11

09 Oct '11

Hi all, I have placed an example of seam carving here: https://github.com/stefanv/scikits.image-1/blob/seam_carving/doc/examples/p… The idea is super simple, but currently it's too slow. I'm curious to see if anyone can improve its execution time? If you haven't seen seam carving before, take a look at the video link in the docstring. Regards Stéfan

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Re: releasing & packaging vs. renaming
by Stéfan van der Walt 09 Oct '11

09 Oct '11

On Sun, Oct 9, 2011 at 2:08 AM, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > > 2011/10/9 Stéfan van der Walt <stefan(a)sun.ac.za> >> >> 2011/10/8 Stéfan van der Walt <stefan(a)sun.ac.za>: >> > On Sat, Oct 8, 2011 at 9:34 PM, Tony Yu <tsyu80(a)gmail.com> wrote: >> >> Agreed: there's definitely a wide range of activity among the scikits. >> >> sklearn and statsmodels are probably a couple of the more active ones, >> >> so >> >> they'd be good examples to follow. And I also agree that changing the >> >> name >> >> sooner, rather than later, would be best. +1 >> > >> > Is there a preference between `skimage` and `skimg` ? >> >> Actually, `ski` is also available. Three letters--not too hard to >> type, doesn't sound awful (es-kay-eye for scikits image), and after >> all--it's just a module name :) > > I don't whether you'd take this in account, but it's quite hard to google. > Googling sklearn directly links to the scikit-learn documentation. > Same with statsmodels. Thanks, that's a valid concern. Seems like skimage is the top vote so far, then. Any other votes? Cheers Stéfan

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scikit-image October 2011