Mailman 3 September 2013 - scikit-image

Re: import error on linux
by Josh Warner 27 Sep '13

27 Sep '13

I ordered a Raspberry Pi-compatible board not long ago, and look forward to when I can test and answer questions like this firsthand. In the meantime, it looks like certain required packages for NumPy and SciPy are not included in the default distribution, and binaries may not be available. It is, however, reported possible to compile and install the required dependencies for Scikit-Image. It may take some time to compile, but it is possible. This blog post may be an excellent place to start. I have not tried if myself yet, but the method looks sound: <http://wyolum.com/numpyscipymatplotlib-on-raspberry-pi/> http://wyolum.com/numpyscipymatplotlib-on-raspberry-pi/ Run the commands from the first group on that page - including the optional bracketed ones - in order. Then, additionally, run: sudo easy_install cython sudo easy_install scikit-image I'm confident this can be done. Let us know if you run into trouble. Josh On Friday, September 27, 2013 8:16:40 AM UTC-5, Stefan van der Walt wrote: On Fri, Sep 27, 2013 at 10:04 AM, Guillaume Gay > <guil...(a)mitotic-machine.org <javascript:>> wrote: > > You really need to be more detailed and specific with your problems. > > But, Guillaume, I don't understand--haven't you also not had success > running skimage on a Raspberry Pi? I know I certainly haven't :) > > Let us know your config and error message, Payal, we'll see what we can > do. > > Happy weekend! > Stéfan >

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Re: Image alignment and feature extraction
by Stuart Mumford 27 Sep '13

27 Sep '13

Hey Ankit, Thanks for your response, it's very helpful. >> b) What the difference between FAST, oFAST and rBRIEF and STAR (and FREAK?) is and which one likely to be the most appropriate for random pictures of the Sun? > > Currently, I cannot answer this question in complete confidence, partly because I am yet to complete and test FREAK and partly because I am not aware of the data, or the kind of solar images that are going to be aligned. Can you give some examples of pairs of images that are required to be aligned in Solar Physics. Some queries that one would have about the data are like : Are the solar images that need to be aligned generated from the same camera but at different time intervals? Generally yes. Sometimes one series of images taken with the same camera at different times is aligned, primarily to compensate for small variation in telescope pointing, and then that is used for other images which are assumed to have the same pointing. >Is the scaling or the zoom factor changing? This would be unlikely. >Is it only the Sun's rotation about its axis that is generating these two different images or some other factor is also involved? Generally solar rotation is compensated for by using models of the rotation rather than image registration. >Currently, ORB is the best bet, because of its speed and invariance to both scaling and rotation. Shiny. > >> c) What else needs to be done to turn this feature detection and description work into registration? > > Image Registration Pipeline can be summarized as : Detect features(keypoints) --> Compute Descriptors --> Match keypoints --> Treat one image as the reference and Estimate the Geometric Transformation required to get the second image using the matches. ORB does the first three and the 4th stage is what needs to be done. These slides[3] explain it better. So the RANSAC algorithm from those slides? Thanks again. Stuart

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Re: Image alignment and feature extraction
by Ankit Agrawal 27 Sep '13

27 Sep '13

Hi Stuart, OK I need to plead ignorance here, is there a decent reference on / can > someone explain to me: > a) what ORB is :p > ORB is a feature detection and description pipeline like SIFT and contains Oriented FAST(oFAST) and Rotated BRIEF(rBRIEF) as its feature detector and feature descriptor respectively. In short, Oriented FAST feature detector is the FAST corner detector computed along with its orientation(which is computed as in [1] Section 3.2). Rotated BRIEF is the BRIEF feature descriptor computed by rotating the test-decision pairs along the orientation of oFAST. Refer [2] and [1]. b) What the difference between FAST, oFAST and rBRIEF and STAR (and FREAK?) > is and which one likely to be the most appropriate for random pictures of > the Sun? > Currently, I cannot answer this question in complete confidence, partly because I am yet to complete and test FREAK and partly because I am not aware of the data, or the kind of solar images that are going to be aligned. Can you give some examples of pairs of images that are required to be aligned in Solar Physics. Some queries that one would have about the data are like : Are the solar images that need to be aligned generated from the same camera but at different time intervals? Is the scaling or the zoom factor changing? Is it only the Sun's rotation about its axis that is generating these two different images or some other factor is also involved? Currently, ORB is the best bet, because of its speed and invariance to both scaling and rotation. c) What else needs to be done to turn this feature detection and > description work into registration? > Image Registration Pipeline can be summarized as : Detect features(keypoints) --> Compute Descriptors --> Match keypoints --> Treat one image as the reference and Estimate the Geometric Transformation required to get the second image using the matches. ORB does the first three and the 4th stage is what needs to be done. These slides[3] explain it better. [1] http://www.vision.cs.chubu.ac.jp/CV-R/pdf/Rublee_iccv2011.pdf [2] http://cvlabwww.epfl.ch/~lepetit/papers/calonder_eccv10.pdf [3] http://cs.haifa.ac.il/hagit/courses/CP/Lectures/CP05_FeaturesRegistX4.pdf

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Re: Image alignment and feature extraction
by Juan Nunez-Iglesias 27 Sep '13

27 Sep '13

To paraphrase the great Dave Barry: Random Pictures of the Sun would be an excellent name for a rock band. =D (Or a blog, failing that!) I'll leave the actual questions to more qualified posters. ;) On Fri, Sep 27, 2013 at 11:18 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: > Hi, > > OK I need to plead ignorance here, is there a decent reference on / can > someone explain to me: > a) what ORB is :p > b) What the difference between FAST, oFAST and rBRIEF and STAR (and > FREAK?) is and which one likely to be the most appropriate for random > pictures of the Sun? > c) What else needs to be done to turn this feature detection and > description work into registration? > > Thanks!! > Stuart > > > On 27 September 2013 14:08, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > >> Hi Stuart >> >> On Fri, Sep 27, 2013 at 2:05 PM, Stuart Mumford <stuart(a)mumford.me.uk> >> wrote: >> > After having spoken to people at scipy this year I have seen a lot of >> work >> > going into feature extraction and description. I was wondering what the >> > status of this was and what still needs to be done before I (/we, >> SunPy) can >> > use it to align our images? >> >> Google Summer of Code is just ending, and Ankit posted the result of >> his and Johannes's work on ORB: >> >> >> http://skimager.blogspot.com/2013/09/oriented-fast-and-rotated-brieforb-hi.… >> >> We also have STAR (Censure) features, so registration is finally within >> reach! >> >> > P.S. expect more emails regarding image warping in the next month ;) >> >> Bring it on! >> >> Cheers >> Stéfan >> >> -- >> 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. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. >

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Re: Image alignment and feature extraction
by Stuart Mumford 27 Sep '13

27 Sep '13

Hi, OK I need to plead ignorance here, is there a decent reference on / can someone explain to me: a) what ORB is :p b) What the difference between FAST, oFAST and rBRIEF and STAR (and FREAK?) is and which one likely to be the most appropriate for random pictures of the Sun? c) What else needs to be done to turn this feature detection and description work into registration? Thanks!! Stuart On 27 September 2013 14:08, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Hi Stuart > > On Fri, Sep 27, 2013 at 2:05 PM, Stuart Mumford <stuart(a)mumford.me.uk> > wrote: > > After having spoken to people at scipy this year I have seen a lot of > work > > going into feature extraction and description. I was wondering what the > > status of this was and what still needs to be done before I (/we, SunPy) > can > > use it to align our images? > > Google Summer of Code is just ending, and Ankit posted the result of > his and Johannes's work on ORB: > > > http://skimager.blogspot.com/2013/09/oriented-fast-and-rotated-brieforb-hi.… > > We also have STAR (Censure) features, so registration is finally within > reach! > > > P.S. expect more emails regarding image warping in the next month ;) > > Bring it on! > > Cheers > Stéfan > > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out. >

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Re: import error on linux
by Guillaume Gay 27 Sep '13

27 Sep '13

Hi Payal, You really need to be more detailed and specific with your problems. What version of linux are you using, what version of python and how did you install skimage? What error message did you get? G. Le 27/09/2013 09:22, Payal Gupta a écrit : > hello.... > > i am using skimage library on raspberry pi which have linux platform > but i cant import skimage module on this. > what do i do? > anybody know this prob. > reply > -- > 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. > For more options, visit https://groups.google.com/groups/opt_out.

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Re: Image alignment and feature extraction
by Stéfan van der Walt 27 Sep '13

27 Sep '13

Hi Stuart On Fri, Sep 27, 2013 at 2:05 PM, Stuart Mumford <stuart(a)mumford.me.uk> wrote: > After having spoken to people at scipy this year I have seen a lot of work > going into feature extraction and description. I was wondering what the > status of this was and what still needs to be done before I (/we, SunPy) can > use it to align our images? Google Summer of Code is just ending, and Ankit posted the result of his and Johannes's work on ORB: http://skimager.blogspot.com/2013/09/oriented-fast-and-rotated-brieforb-hi.… We also have STAR (Censure) features, so registration is finally within reach! > P.S. expect more emails regarding image warping in the next month ;) Bring it on! Cheers Stéfan

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Image alignment and feature extraction
by Stuart Mumford 27 Sep '13

27 Sep '13

Hello, After having spoken to people at scipy this year I have seen a lot of work going into feature extraction and description. I was wondering what the status of this was and what still needs to be done before I (/we, SunPy) can use it to align our images? Stuart P.S. expect more emails regarding image warping in the next month ;)

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import error on linux
by Payal Gupta 27 Sep '13

27 Sep '13

hello.... i am using skimage library on raspberry pi which have linux platform but i cant import skimage module on this. what do i do? anybody know this prob. reply

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Re: ndarray subclasses
by Stéfan van der Walt 24 Sep '13

24 Sep '13

On Mon, 23 Sep 2013 10:43:42 -0500, Thomas A Caswell wrote: > My concern with this proposal is now the user has two independent ways to > pass in the same information. If inconsistent information is passed in the > library has to make a decision about which one takes precedence. This adds > to the complexity of the function and can only lead to confusion on the > part of the users when they think the precedence should have the opposite > order. Let's postpone this API decision until we have more certainty on how it'd be used. For now, my_func(image, sampling=image.sampling) is quite adequate. It still allows the user to add sampling information to their images, if they'd so wish. StÃ¯Â¿Â½fan

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