Mailman 3 January 2016 - scikit-image

Re: skimage and opencv
by Emmanuelle Gouillart 22 Sep '16

22 Sep '16

Hi FranÃ¯Â¿Â½ois, that's an excellent question, and not a troll :-). Opencv is a very powerful library, but it focuses primarily on computer vision (feature detection and extraction, classification, ...), as opposed to image processing in general (with other tasks such as denoising, segmentation, ...). The other big difference is that skimage builds on numpy ndarrays, and uses the full power of the numpy API (including of course the basic facilities for processing arrays as images that come with numpy), as well as some of scipy functions (you could have added scipy.ndimage to your list -- a few functions in skimage are wrappers around scipy.ndimage, that exist for the sake of completeneness). One important consequence is that algorithms working for 3-d or even n-d images can be easily implemented in 3-d/n-d in skimage, whereas opencv is restricted to 2-D images (as far as I know). Thanks to the use of numpy arrays, the API of skimage is also quite pleasant for a numpy user, more than the API of opencv. A related difference is that skimage is written in python and cython, whereas opencv is a C++ library. The two libraries attract a different crowd of developers, and a Python/Cython toolkit based on numpy arrays is easier to develop and maintain inside the Scientific Python ecosystem. I'm sure that other devs/users will have things to add to this discussion! Cheers, Emmanuelle On Thu, Dec 27, 2012 at 02:06:08PM -0800, FranÃ¯Â¿Â½ois wrote: > Hi users and devs, > It came to my knowledge that another python library (based on C++ and C > codes) for image processing exists too : opencv > I understand that numpy intregrates some basic features and we need some > advanced features but I have the feeling that skimages is redoundant with > opencv in some ways. > What's the position of skimage about that? (Don't read this question as a > troll but like a real question). > I mean that similar features exist in both. Would not be possible to > reuse/integrate opencv or merge? what's the reason for keeping them apart? > My observation is there is 4 libraries to manipulate images: > * PIL > * numpy > * skimages > * opencv > That's a lot. > Cheers,

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Boundary/outline of objects in an Image
by ashz＠walla.co.il 15 Feb '16

15 Feb '16

Hi, I try to focus on scikit-image instead of other non-open source software. Therefore, is there an example how to boundary/outline of objects in an Image? Something like this tutorial: http://www.mathworks.com/help/images/boundary-tracing-in-images.html Thanks

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Re: 0.12 release
by Emmanuelle Gouillart 03 Feb '16

03 Feb '16

One more request, especially to the core team: could we restrain ourselves from adding new PRs to the 0.12 milestone, except for bad bug fixes? We need to converge at some point :-). Emma On Sun, Jan 31, 2016 at 09:52:25AM -0800, StÃ©fan van der Walt wrote: > On 31 January 2016 at 08:58, Emmanuelle Gouillart > <emmanuelle.gouillart(a)nsup.org> wrote: > >> > StÃ©fan, do you want these PRs to be merged for 0.12? Can you estimate > >> > when they should be ready? > > > >> I'll make the last changes to those PRs now. If, after that, they are > >> not ready to merge, let us not hold up the whole release. > > I've made updates to those PRs. Unfortunately, I will be out for most > of the rest of the day, but feel free to update those PRs--I've added > Emma, Johannes, Josh and Juan as collaborators on my fork. > > Thanks again! > > StÃ©fan > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe(a)googlegroups.com. > To post to this group, send an email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQk7emQRwk9W5-sRZ0nq8gS…. > For more options, visit https://groups.google.com/d/optout.

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Re: 0.12 release
by Emmanuelle Gouillart 31 Jan '16

31 Jan '16

> > StÃ©fan, do you want these PRs to be merged for 0.12? Can you estimate > > when they should be ready? > I'll make the last changes to those PRs now. If, after that, they are > not ready to merge, let us not hold up the whole release. Awesome! From GitHub's activity there are several devs around today, so we should be able to review and hopefully merge today. > > I can take care of the release process as described in our RELEASE.txt, > > but it would be the first time for me so I'll probably need some help > > along the process! > That is very kind of you! I am happy to lend a hand as and where needed. Thanks! Emma

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Re: 0.12 release
by Emmanuelle Gouillart 31 Jan '16

31 Jan '16

We only have 3 PRs started by StÃ©fan marked for 0.12, so we're indeed very close! Out of these 3, 2 are almost ready to merge, and the last one (about the novice module) could be postponed to 0.13 without much damage (if I'm not mistaken; StÃ©fan, you might have a different opinion). StÃ©fan, do you want these PRs to be merged for 0.12? Can you estimate when they should be ready? I can take care of the release process as described in our RELEASE.txt, but it would be the first time for me so I'll probably need some help along the process! Best, Emma On Thu, Jan 21, 2016 at 06:04:11PM -0800, StÃ©fan van der Walt wrote: > On Wed, Jan 20, 2016 at 1:18 PM, Johannes SchÃ¶nberger <jsch(a)demuc.de> wrote: > > It's been a while since we had a release and lots of great stuff has been merged in the mean time. I suggest to freeze any other PRs until we release 0.12. Maybe we can aim to release 0.12 in the next days? > Yes, we're very close now! We're starting to see the effect of the > package & userbase growing: in the past, we'd release, and people > would come back with a few bug reports. Now, simply planning a > release triggers new bug reports, making the milestone grow and grow! > But the list is now shrinking rapidly. > Thanks all for your hard work! > StÃ©fan

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Re: How to apply/attach a colormap from an image to another image
by Matteo Niccoli 29 Jan '16

29 Jan '16

First off, thanks Joe Your code is what I was looking for - AND, it sounds like - the thing to do, unless one wanted to embark in the kind of regression Matthias suggests. Second, Stéfan, sorry for the confusion about the rainbowbot, that was an aside, I happened to post on both of them at the same time, but really the Jupiter idea was more because I was playing with image size reduction via conversion to intensity and component reduction via PCA, and was wondering how one could compare the quality of the result with the input image, but in color as opposed to in grayscale. Matthias, I think it would be fun to work together on the rainbowbot idea, and then to send those 'viridize' tweets. I'll send you an email with some ideas. Cheers, Matteo On Thu, Jan 28, 2016 at 3:33 PM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > > On Thu, Jan 28, 2016 at 1:29 PM, Joe Kington <joferkington(a)gmail.com> > wrote: > > >> I was the one Matteo mentioned on the slack group. At first I thought >> Matteo was referring to exactly what you described: Take a colormapped >> single-band image and unmap/remap the color palette. >> > > In one of the threads here, I read > > """ > > My idea would be to make it into a web app called 'rainbowbot' which would > automatically detect bad colormaps either form online images or user > uploaded images, and then provide them with tools to either equalize the > colormaps or replace with a perceptual version with same hue range, or..... > > It is in here > > https://github.com/mycarta/rainbowbot > I am open to suggestions, and offers to collaborate. > """ > > Otherwise, I guess the problem is as simple as: > > image = color.rgb2gray(io.imread('image.jpg')) > plt.imshow(image, cmap='viridis') > > If it is about turning false color maps into true color maps, that would > be hard, given the many mappings out there. > > Stéfan > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/jxD0GTK_8B4/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > To post to this group, send email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CABDkGQm59%2BHikycM3uxJpEw_k… > <https://groups.google.com/d/msgid/scikit-image/CABDkGQm59%2BHikycM3uxJpEw_k…> > . > > For more options, visit https://groups.google.com/d/optout. >

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How to apply/attach a colormap from an image to another image
by Matteo 29 Jan '16

29 Jan '16

Can something like this (which by the way I can't get to work) be done using scikit-image? http://stackoverflow.com/questions/3114925/pil-convert-rgb-image-to-a-speci… I've done similar things in Matlab before: https://mycarta.wordpress.com/2012/04/05/visualization-tips-for-geoscientis… but I'd really like to be able to do it in Python. What I would like to do currently is: 1) Import an RGB image, which would have its own colormap - say this one for example: https://upload.wikimedia.org/wikipedia/commons/b/b3/Jupiter_new_hubble_view… 2) convert it to intensity, say like this: intnst = 0.2989 * rgb[:,0] + 0.5870 * rgb[:,1] + 0.1140 * rgb[:,2] # get the intensityintensity = np.rint(intnst) # rounds up to nearest integer 3) display the intensity color-mapped to the same colours the original RGB had. Any tips, ideally withrcode or pseudocode would be greatly appreciated. Thanks, Matteo

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MSER implementation
by Vighnesh Birodkar 29 Jan '16

29 Jan '16

Hello guys I wanted to start on the implementation of the MSER[1] blob detection algorithm. I am leaning towards implementing the approach of the original paper[2], which has a linear time complexity for all practical images. The alternative is a guaranteed linear time implementation[2], but the paper does not have as many citations. Any thoughts are welcome. [1] : https://en.wikipedia.org/wiki/Maximally_stable_extremal_regions [2] : https://www.robots.ox.ac.uk/~vgg/research/affine/det_eval_files/matas_bmvc2… [3] : http://link.springer.com/chapter/10.1007%2F978-3-540-88688-4_14 Thanks Vighnesh

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Fwd: [Numpy-discussion] Bump warning stacklevel
by Stéfan van der Walt 27 Jan '16

27 Jan '16

Devs, please note the thread below. ---------- Forwarded message ---------- From: Sebastian Berg <sebastian(a)sipsolutions.net> Date: Wed, Jan 27, 2016 at 10:26 AM Subject: [Numpy-discussion] Bump warning stacklevel To: Discussion of Numerical Python <numpy-discussion(a)scipy.org> Hi all, in my PR about warnings suppression, I currently also have a commit which bumps the warning stacklevel to two (or three), i.e. use: warnings.warn(..., stacklevel=2) (almost) everywhere. This means that for example (take only the empty warning): np.mean([]) would not print: /usr/lib/python2.7/dist-packages/numpy/core/_methods.py:55: RuntimeWarning: Mean of empty slice. warnings.warn("Mean of empty slice.", RuntimeWarning) but instead print the actual `np.mean([])` code line (the repetition of the warning command is always a bit funny). The advantage is nicer printing for the user. The disadvantage would probably mostly be that existing warning filters that use the `module` keyword argument, will fail. Any objections/thoughts about doing this change to try to better report the offending code line? Frankly, I am not sure whether there might be a python standard about this, but I would expect that for a library such as numpy, it makes sense to change. But, if downstream uses warning filters with modules, we might want to reconsider for example. - Sebastian _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion(a)scipy.org https://mail.scipy.org/mailman/listinfo/numpy-discussion

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Re: template matching - ValueError: image must be 2d / 3d array
by Anurag 24 Jan '16

24 Jan '16

turns out, it was bug in my code, the following snippet works: https://gist.github.com/anuragphadke/56a3be21128852f69031 -anurag On Sat, Jan 23, 2016 at 5:06 PM, Anurag <anurag.phadke(a)gmail.com> wrote: > Hello, > I am trying to run Template Matching code as mentioned in > http://scikit-image.org/docs/dev/auto_examples/plot_template.html, > however, on trying to read an image from file, it returns the following > error: > ValueError: The parameter `image` must be a 2-or-3-dimensional array > > full gist and Traceback at: > https://gist.github.com/anuragphadke/48b8565a6bcaa477daa5 > > Any tips on what I might be doing wrong here? tried converting image to > grayscale etc. > > > -- > Twitter: @anuragphadke (https://twitter.com/#!/anuragphadke) > -- Twitter: @anuragphadke (https://twitter.com/#!/anuragphadke)

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