Mailman 3 August 2012 - scikit-image

Re: Multispectral random walker segmentation
by Emmanuelle Gouillart 18 Sep '12

18 Sep '12

Hi Josh, extending the random walker algorithm to multichannel images sounds like a very nice idea, and I'm sure that it would be useful for other people (including myself!). In fact, I had started working on some improvements of the random walker code but didn't go as far as proposing the pull request. I have a branch for that on https://github.com/emmanuelle/scikits.image/tree/fix_random_walker, maybe you can include these changes when you contribute your changes? Cheers, Emmanuelle On Mon, Aug 20, 2012 at 10:03:53AM -0700, Josh Warner wrote: > I have modified the existing random walker algorithm into a fully > backwards-compatible version which allows inclusion of multispectral data, > e.g. RGBA channels or different (registered) image modalities. Ã¯Â¿Â½I really > liked the existing algorithm, so I just extended it rather than write one > from scratch for my own purposes. Ã¯Â¿Â½The overhead is minimal; multispectral > processing is triggered if data is passed as an iterable of arrays rather > than just an array. Ã¯Â¿Â½ > This amounts to combining image gradients as sqrt(sum-of-squares) and > dividing by sqrt(#channels). Ã¯Â¿Â½For obvious reasons, the several channels > must be pre-processed to have data on similar ranges by whitening or a > similar method. Ã¯Â¿Â½Not usually a problem for RGB, but in medical imaging > this rears its head. > Would this be of interest to the community? Ã¯Â¿Â½I'd be happy to contribute > the changes if there is interest.

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Timing comparisons between mahotas & scikits-image
by Luis Pedro Coelho 06 Sep '12

06 Sep '12

Hello, In the context of my previous email to pythonvision https://groups.google.com/d/topic/pythonvision/SSCF4LUlRKQ/discussion I made a timing comparison between mahotas & scikits-image. operation | mahotas | pymorph | skimage ------------+----------+----------+--------- erode | 10.80 | 14.33 | 80.17 dilate | 11.44 | 8.93 | 41.59 open | 22.45 | 23.20 | 80.18 center mass | 7.05 | NA | NA sobel | 75.03 | NA | 105.72 cwatershed | 201.03 | 56586.50 | 290.41 daubechies | 19.05 | NA | NA haralick | 306.48 | NA | 7391.37 (Best viewed with fixed-width fonts) The unit of measurement is the time it takes to run ``numpy.max(image)`` Mahotas is always faster than skimage (although pymorph is better for certain morphological basic operations). I used GCLM in skimage to stand for Haralick, which is a rough approximation. I attach the script that generates these (against github skimage). If you think that I have used skimage incorrectly, please let me know. Best, -- Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org

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Re: Geometric transformations
by Tim Sheerman-Chase 01 Sep '12

01 Sep '12

Stéfan, I found scikits-image is using quite a different approach than my version but I think I have it mostly working now! https://github.com/scikits-image/scikits-image/pull/286 Regards, Tim

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Re: Geometric transformations
by Stéfan van der Walt 31 Aug '12

31 Aug '12

Hi Tim On Aug 31, 2012 3:48 PM, "Tim Sheerman-Chase" <timsc60(a)googlemail.com> wrote: > > Hi all, > > I just implemented a stand alone piecewise affine image warp function. A friend pointed me at this project and said you might be interested. I noticed this thread on the recently merged geometric transforms. It seems to include an affine transform function. I wondered if it would be worth extending the new affine transform in scikits-image to also handle piecewise affine? > > https://github.com/TimSC/image-piecewise-affine > > Any thoughts? Thanks for getting in touch; we are definitely interested! I think you'll find it easy to integrate your code with our warp module.. All you need to specify is a coordinate transformation. Would you like to have a look at our code as well? We'd gladly work with you to get this integrated. Regards Stéfan

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Re: Funding proposal
by Andreas Mueller 30 Aug '12

30 Aug '12

Hi Stefan. In principle I'd be interested and if you don't find any one else, I can volunteer. The only issue is that I am super swamped. But for funding skimage, I'm sure I could make some room ;) Cheers, Andy On 08/29/2012 03:56 PM, StÃ¯Â¿Â½fan van der Walt wrote: > Hi everyone > > There is an opportunity to apply for some funding, and I'd like to > know who'd be interested to co-author the grant. I started a Google > document for this purpose, so let me know and I will add you. > > Here's to a healthy and well-funded skimage! > > StÃ¯Â¿Â½fan

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Funding proposal
by Stéfan van der Walt 29 Aug '12

29 Aug '12

Hi everyone There is an opportunity to apply for some funding, and I'd like to know who'd be interested to co-author the grant. I started a Google document for this purpose, so let me know and I will add you. Here's to a healthy and well-funded skimage! Stéfan

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inconsistency between label and regionprops
by Emmanuelle Gouillart 27 Aug '12

27 Aug '12

Hello, regionsprops only measures the properties of region labeled with strictly positive labels (since it uses ndimage.find_objects). However, when using skimage's label with the background keyword argument, the background pixels are labeled with -1, so that there is one foreground region labeled with the label 0. This region will not be taken into account by regionprops. This behaviour can be fixed easily in regionprops, but wouldn't it be better to label background pixels with 0? Cheers, Emmanuelle

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Re: bug in regionprops underlying library qhull?
by Luca Fiaschi 27 Aug '12

27 Aug '12

Hi Stefan, I do not know well the algorithm that qhul implements, and it is lucky to be more complicated than what is needed in this case since it seems to work in higher dimensions than 2D. Nevertheless, I do not see any reason why the points should be pathological: here my modifications: --- a/skimage/morphology/convex_hull.py +++ b/skimage/morphology/convex_hull.py @@ -51,9 +51,15 @@ def convex_hull_image(image): 'scipy >= 0.9.') # Find the convex hull - chull = Delaunay(coords).convex_hull - v = coords[np.unique(chull)] + #chull = Delaunay(coords).convex_hull + #v1 = coords[np.unique(chull)] + import vigra + v=vigra.geometry.convexHull(np.copy(coords).astype(np.float32)).view(np.ndarray) + #print v1 + #print v2 + #raise As you can see I just exchanged the computation from scipy with that of another library to which I personally had contributed implementing the standard monotone chain convex hull algorithm. Everything seems fine now. Il giorno venerdì 24 agosto 2012 13:43:43 UTC+2, Stefan van der Walt ha scritto: > > Hi Luca > > On Wed, Aug 22, 2012 at 1:41 AM, Luca Fiaschi <luca.f...(a)gmail.com<javascript:>> > wrote: > > I confirm the bug to be really in qhull. > > I substituted the computation of the convex hull in scipy (qhull) with > > another library (vigranumpy) and thins fix the problem. > > Strange, do you know if the points are pathological for some reason? > Perhaps we can pre-filter them to prevent any crashes. Where did you > get these coordinates from? > > Stéfan >

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Re: Fwd: Sprint
by Andreas Mueller 26 Aug '12

26 Aug '12

Nice. I guess they work a lot like SLIC, only they put more emphasis on the (x,y) space. On 08/26/2012 03:29 PM, StÃ¯Â¿Â½fan van der Walt wrote: > Andreas, look at these nifty super-pixels :) > > ---------- Forwarded message ---------- > From: *Nicolas Rougier* > Date: Sun, Aug 26, 2012 at 6:26 AM > Subject: Re: Sprint > > Cool. > > Also, I forgot a probably useless filter based on voronoi cells. Just > don't know if it might be of some interest or not for scikit-image: > Code at: https://github.com/rougier/gallery (showcase/showcase-9.py) > > > Nicolas

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Fwd: Sprint
by Stéfan van der Walt 26 Aug '12

26 Aug '12

Andreas, look at these nifty super-pixels :) ---------- Forwarded message ---------- From: Nicolas Rougier Date: Sun, Aug 26, 2012 at 6:26 AM Subject: Re: Sprint Cool. Also, I forgot a probably useless filter based on voronoi cells. Just don't know if it might be of some interest or not for scikit-image: Code at: https://github.com/rougier/gallery (showcase/showcase-9.py) Nicolas

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