Mailman 3 February 2014 - scikit-image

Re: Google Summer of Code 2014
by Stéfan van der Walt 18 Feb '14

18 Feb '14

On Tue, Feb 18, 2014 at 5:53 PM, abid rahman <abidrahman2(a)gmail.com> wrote: > So I think SWT is patented, isn't it? I'm not sure--I would like to contact the researchers in Microsoft to get clarity (or perhaps someone would volunteer to do so?) > I wonder if implementation of this paper is considered to be a GSoC project, > I would like to work on it. I think so--the goal is text detection, not to implement any specific algorithm (I updated the project description to include this paper). > Another question : What is the status of SIMD optimization in scikit-image? > Does Cython support such kind of optimization works? Is there any SIMD > optimized functions available in scikit-image? These are the only vectorized ops we have: https://github.com/scikit-image/scikit-image/blob/master/skimage/_shared/ve… Stéfan

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Re: Google Summer of Code 2014
by abid rahman 18 Feb '14

18 Feb '14

Hi Stefan, So I think SWT is patented, isn't it? That looks fantastic--algorithms such as these are exactly what I had in > mind. > I wonder if implementation of this paper is considered to be a GSoC project, I would like to work on it. *Another question* : What is the status of SIMD optimization in scikit-image? Does Cython support such kind of optimization works? Is there any SIMD optimized functions available in scikit-image? Regards Abid K

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Re: Google Summer of Code 2014
by Stéfan van der Walt 18 Feb '14

18 Feb '14

On Tue, Feb 18, 2014 at 6:15 AM, abid rahman <abidrahman2(a)gmail.com> wrote: > And I think that may be the reason OpenCV went after another (newer - CVPR > 2012) algorithm for same : > http://cmp.felk.cvut.cz/~neumalu1/neumann-cvpr2012.pdf That looks fantastic--algorithms such as these are exactly what I had in mind. Stéfan

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Re: Face detection
by Vasanth Kalingeri 18 Feb '14

18 Feb '14

Hi Stéfan, I am a computer science undergrad, presently in my second year and extremely interested in machine learning and computer vision. I found the project that you mentioned, here <https://github.com/scikit-image/scikit-image/wiki/GSoC-2014>and I find it to be really interesting to work on. I have used the haar classifier for detecting faces(mostly as a black box) and I would like to understand its working so that I can work on this project, can you please let me know how I start with this? Any good algorithms in recent research papers that I have to read? or any essential prerequisites for the project? Thanks a lot in advance. Vasanth Kalingeri On Thursday, March 28, 2013 3:05:31 PM UTC+5:30, Stefan van der Walt wrote: > > Hi everyone > > I've been interested in getting face detection into skimage for a > while. This morning, Nathan Faggian reminded me that the highly > popular Viola-Jones detector is patent encumbered (yes, if you're not > careful you can use patented code in packages like OpenCV). However, > the following link seems to suggest that we can work around that by > training our own classifier with different features: > > > http://rafaelmizrahi.blogspot.com/2007/02/intel-opencv-face-detection-licen… > > If there's any interest in working on this, or if you already have an > algorithm available, please get in touch. > > Stéfan >

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Re: Google Summer of Code 2014
by abid rahman 18 Feb '14

18 Feb '14

Hi Stefan, Here is *one link of patent application* I just found out (I am not sure if it is proof for whether it is patented. I don't know much about patents, but I think you will understand it) : http://www.faqs.org/patents/app/20090285482 Long back, I have seen a video its author presenting SWT in a conference, and a question came from audiance about its source code, He replied "come to Microsoft, you will get the code". "Otherwise?", "It is not upto me" Please *watch last one minute of this video* : http://videolectures.net/cvpr2010_epshtein_dtns/ Some two years back, when I first saw this paper, I had a plan to implement it (and contribute to OpenCV actually). So while gathering more information about this, I saw this video, and I assumed it is patented and OpenCV won't take it. So left the plan there. And I think that may be the reason *OpenCV went after another (newer - CVPR 2012) algorithm for same* : http://cmp.felk.cvut.cz/~neumalu1/neumann-cvpr2012.pdf Regards Abid K. On Mon, Feb 17, 2014 at 7:22 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Abid > > On Sun, Feb 16, 2014 at 5:58 PM, abid rahman <abidrahman2(a)gmail.com> > wrote: > > One question. Isn't stroke width transform patented by microsoft > research? > > I haven't seen any indication that it is; could you provide me with a > reference? > > 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: Digitization errors in small circles
by Adam Hughes 18 Feb '14

18 Feb '14

On Monday, February 17, 2014 8:14:10 PM UTC-5, Juan Nunez-Iglesias wrote: > > Your first error is the circularity of a square of side 1, which according > to your formula should be 4 * pi * 1 / (4^2) = pi / 4 ≈ 0.785. > Doh! Duh, right. > > I don't know anything about the Canvas object so I'll let others comment > on the rest, but clearly this is very dependent on how perimeter is > computed: are we computing the perimeter of a polygon with the boundary > vertices of the rasterization, or the perimeter along the (square) pixel > boundaries, or the *convex* polygon enveloping the rasterized circle? Based > on your numbers, I'd bet on one of the first two. Again, I'll let someone > else deal with the correctness of the approach. =) > Canvas is actually just wrapping skimage.draw and region_props, so it uses the same rasterization that scikit image uses when a user draws a circle. Here's an example that uses pure scikit: http://nbviewer.ipython.org/github/hugadams/pyparty/blob/digitiaztion_help/… I'm pretty sure that the results in the canvas are correct for the plotted circularity. Assuming that the calls to skimage.draw() are correct, would you know which *perimeter* of the methods you listed would be returned by region_props? Thanks Juan > Juan. > > > > On Tue, Feb 18, 2014 at 11:35 AM, Adam Hughes <hughes...(a)gmail.com<javascript:> > > wrote: > >> Hi, >> >> I was trying to measure the circularity as a function of circle radius >> using the underlying circle object from skimage.draw(). I got some strange >> results, and tried to outline the exercise as well as the confusing outcome >> in a notebook. Essentially, the circularity as a function of particle >> radius does not seem to converge to 1.0, and in addition, at very small >> radii, the circularity does not agree with what one would expect from the >> circularity of a pixel (ie rectangle). >> >> I was hoping that an expert could have a glance at the notebook and offer >> some feedback? Hoping that I made an obvious mistake or assertion >> somewhere. >> >> The notebook actually uses my "pyparty" library that I posted a while >> back for drawing and storing the descriptors; however, I verified that >> these are the same descriptors that one gets using skimage.labels() >> directly (this is not show in the notebook). >> >> Here's the static view: >> >> >> http://nbviewer.ipython.org/github/hugadams/pyparty/blob/master/examples/No… >> >> Thanks. >> >> -- >> 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...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/groups/opt_out. >> > >

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Re: Digitization errors in small circles
by Juan Nunez-Iglesias 18 Feb '14

18 Feb '14

Your first error is the circularity of a square of side 1, which according to your formula should be 4 * pi * 1 / (4^2) = pi / 4 ≈ 0.785. I don't know anything about the Canvas object so I'll let others comment on the rest, but clearly this is very dependent on how perimeter is computed: are we computing the perimeter of a polygon with the boundary vertices of the rasterization, or the perimeter along the (square) pixel boundaries, or the *convex* polygon enveloping the rasterized circle? Based on your numbers, I'd bet on one of the first two. Again, I'll let someone else deal with the correctness of the approach. =) Juan. On Tue, Feb 18, 2014 at 11:35 AM, Adam Hughes <hughesadam87(a)gmail.com>wrote: > Hi, > > I was trying to measure the circularity as a function of circle radius > using the underlying circle object from skimage.draw(). I got some strange > results, and tried to outline the exercise as well as the confusing outcome > in a notebook. Essentially, the circularity as a function of particle > radius does not seem to converge to 1.0, and in addition, at very small > radii, the circularity does not agree with what one would expect from the > circularity of a pixel (ie rectangle). > > I was hoping that an expert could have a glance at the notebook and offer > some feedback? Hoping that I made an obvious mistake or assertion > somewhere. > > The notebook actually uses my "pyparty" library that I posted a while back > for drawing and storing the descriptors; however, I verified that these are > the same descriptors that one gets using skimage.labels() directly (this is > not show in the notebook). > > Here's the static view: > > > http://nbviewer.ipython.org/github/hugadams/pyparty/blob/master/examples/No… > > Thanks. > > -- > 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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Digitization errors in small circles
by Adam Hughes 18 Feb '14

18 Feb '14

Hi, I was trying to measure the circularity as a function of circle radius using the underlying circle object from skimage.draw(). I got some strange results, and tried to outline the exercise as well as the confusing outcome in a notebook. Essentially, the circularity as a function of particle radius does not seem to converge to 1.0, and in addition, at very small radii, the circularity does not agree with what one would expect from the circularity of a pixel (ie rectangle). I was hoping that an expert could have a glance at the notebook and offer some feedback? Hoping that I made an obvious mistake or assertion somewhere. The notebook actually uses my "pyparty" library that I posted a while back for drawing and storing the descriptors; however, I verified that these are the same descriptors that one gets using skimage.labels() directly (this is not show in the notebook). Here's the static view: http://nbviewer.ipython.org/github/hugadams/pyparty/blob/master/examples/No… Thanks.

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Re: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Johannes Schönberger 17 Feb '14

17 Feb '14

Does anyone of you plan to go? On 16.02.2014, at 10:22, Anthony Scopatz <scopatz(a)gmail.com> wrote: Hello All! I am pleased to announce that *SciPy 2014*, the thirteenth annual *Scientific Computing with Python conference*, will be held this July 6th-12th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from all types of organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. For more information please visit our website: https://conference.scipy.org/scipy2014/ This year the conference has been extended to include an additional day of presentations. During the presentation days SciPy is proud to host the following event and talk types: - Keynotes - Expert Panels - Short Talks - Poster Presentations - Birds of a Feather Sessions The full program will consist of two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. This year, we are excited to present a job fair for the first time! <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Specialized Tracks This year we are happy to announce two specialized tracks that run in parallel to the general conference: *Scientific Computing in Education* Thanks to efforts such as Software Carpentry, the Hacker Within and grassroots Python Bootcamps, teaching scientific computing as a discipline is becoming more widely accepted and recognized as a crucial task in developing scientific literacy. This special track will focus on efforts to promote and develop scientific computing education, as well as related topics such as reproducibility and best practices for scientific computing. *Geospatial Data in Science* Python has become a core component of organiziing, understanding, and visualizing geospatial data. This track will focus on libraries, tools and techniques for processing Geospatial data of all types and for all purposes -- from low-volume to high-volume, local and global. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Domain-specific Mini-symposia Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. Mini-symposia on the following topics will take place this year: - Astronomy and astrophysics - Bioinformatics - Geophysics - Vision, Visualization, and Imaging - Computational Social Science and Digital Humanities - Engineering <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…> Tutorials Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, which target specifically programmers with no prior knowledge of scientific python. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Developer Sprints A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. The conference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and receive tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Birds-of-a-Feather (BOF) Sessions Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Important Dates - March 14th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. - April 17th: Speakers selected - April 22nd: Sponsorship acceptance deadline - May 1st: Speaker schedule announced - May 6th, or 150 registrants: Early-bird registration ends - July 6-12th: 2 days of tutorials, 3 days of conference, 2 days of sprints We look forward to a very exciting conference and hope to see you all in Austin this summer! The SciPy2014 Organizers -- 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: Google Summer of Code 2014
by Stéfan van der Walt 17 Feb '14

17 Feb '14

Hi Abid On Sun, Feb 16, 2014 at 5:58 PM, abid rahman <abidrahman2(a)gmail.com> wrote: > One question. Isn't stroke width transform patented by microsoft research? I haven't seen any indication that it is; could you provide me with a reference? Stéfan

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Re: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Juan Nunez-Iglesias 17 Feb '14

17 Feb '14

I'd definitely be up for that. =) On Mon, Feb 17, 2014 at 4:10 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > On Sun, Feb 16, 2014 at 6:55 PM, Johannes Schönberger <jsch(a)demuc.de>wrote: > >> Maybe, I'll finally make it as I am not too far off... but not yet sure >> about time and money :-) >> >> Hi Johannes, > > It doesn't look like the page is up yet, but there should be sponsorships > available, and you should definitely apply. (I was sponsored for my trip 2 > years ago.) > > Were you thinking of doing a scikit-image presentation, or possibly even a > tutorial? I was entertaining the idea of submitting a scikit-image tutorial > proposal (again), in case you're interested working together on something > (same to you, Juan). > > -Tony > > -- > 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: ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Johannes Schönberger 17 Feb '14

17 Feb '14

Maybe, I'll finally make it as I am not too far off... but not yet sure about time and money :-) On Feb 16, 2014, at 19:50, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > I very much intend to go, yes. Who am I seeing there??? =) > > > > On Mon, Feb 17, 2014 at 4:11 AM, Johannes Schönberger <jsch(a)demuc.de> wrote: > Does anyone of you plan to go? > > On 16.02.2014, at 10:22, Anthony Scopatz <scopatz(a)gmail.com> wrote: > >> Hello All! >> >> I am pleased to announce that SciPy 2014, the thirteenth annual Scientific Computing with Python conference, will be held this July 6th-12th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from all types of organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. >> For more information please visit our website: https://conference.scipy.org/scipy2014/ >> This year the conference has been extended to include an additional day of presentations. During the presentation days SciPy is proud to host the following event and talk types: >> >> • Keynotes >> • Expert Panels >> • Short Talks >> • Poster Presentations >> • Birds of a Feather Sessions >> The full program will consist of two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. This year, we are excited to present a job fair for the first time! >> >> Specialized Tracks >> This year we are happy to announce two specialized tracks that run in parallel to the general conference: >> >> Scientific Computing in Education >> >> Thanks to efforts such as Software Carpentry, the Hacker Within and grassroots Python Bootcamps, teaching scientific computing as a discipline is becoming more widely accepted and recognized as a crucial task in developing scientific literacy. This special track will focus on efforts to promote and develop scientific computing education, as well as related topics such as reproducibility and best practices for scientific computing. >> >> Geospatial Data in Science >> >> Python has become a core component of organiziing, understanding, and visualizing geospatial data. This track will focus on libraries, tools and techniques for processing Geospatial data of all types and for all purposes -- from low-volume to high-volume, local and global. >> >> Domain-specific Mini-symposia >> Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. >> >> Mini-symposia on the following topics will take place this year: >> >> • Astronomy and astrophysics >> • Bioinformatics >> • Geophysics >> • Vision, Visualization, and Imaging >> • Computational Social Science and Digital Humanities >> • Engineering >> Tutorials >> Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, which target specifically programmers with no prior knowledge of scientific python. >> >> Developer Sprints >> A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. The conference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and receive tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. >> >> Birds-of-a-Feather (BOF) Sessions >> Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. >> >> Important Dates >> • March 14th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. >> • April 17th: Speakers selected >> • April 22nd: Sponsorship acceptance deadline >> • May 1st: Speaker schedule announced >> • May 6th, or 150 registrants: Early-bird registration ends >> • July 6-12th: 2 days of tutorials, 3 days of conference, 2 days of sprints >> We look forward to a very exciting conference and hope to see you all in Austin this summer! >> >> The SciPy2014 Organizers >> >> >> -- >> 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. > > > -- > 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: Google Summer of Code 2014
by Xuejian Rong 16 Feb '14

16 Feb '14

That's great! Currently I'm doing research on computational photography with scikit-image, it's very helpful. I'm trying to make some contributions to the project, especially in the area of deblurring and denoising. On Thursday, February 13, 2014 4:46:48 PM UTC-5, Stefan van der Walt wrote: > > Hi everyone > > If everything goes well, we'll be able to participate in this year's > Google Summer of Code under the PSF umbrella. I've put up a page with > ideas: > > https://github.com/scikit-image/scikit-image/wiki/GSoC-2014 > > Please have a look at it and edit as you see fit. > > Students, if you are interested in participating, now would be a great > time to put in a few pull requests and to take part in conversations > on the mailing list. > > Regards > Stéfan >

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ANN: SciPy 2014 Conference, July 6th - 12th, Austin, TX!
by Anthony Scopatz 16 Feb '14

16 Feb '14

Hello All! I am pleased to announce that *SciPy 2014*, the thirteenth annual *Scientific Computing with Python conference*, will be held this July 6th-12th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from all types of organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. For more information please visit our website: https://conference.scipy.org/scipy2014/ This year the conference has been extended to include an additional day of presentations. During the presentation days SciPy is proud to host the following event and talk types: - Keynotes - Expert Panels - Short Talks - Poster Presentations - Birds of a Feather Sessions The full program will consist of two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. This year, we are excited to present a job fair for the first time! <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Specialized Tracks This year we are happy to announce two specialized tracks that run in parallel to the general conference: *Scientific Computing in Education* Thanks to efforts such as Software Carpentry, the Hacker Within and grassroots Python Bootcamps, teaching scientific computing as a discipline is becoming more widely accepted and recognized as a crucial task in developing scientific literacy. This special track will focus on efforts to promote and develop scientific computing education, as well as related topics such as reproducibility and best practices for scientific computing. *Geospatial Data in Science* Python has become a core component of organiziing, understanding, and visualizing geospatial data. This track will focus on libraries, tools and techniques for processing Geospatial data of all types and for all purposes -- from low-volume to high-volume, local and global. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Domain-specific Mini-symposia Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. Mini-symposia on the following topics will take place this year: - Astronomy and astrophysics - Bioinformatics - Geophysics - Vision, Visualization, and Imaging - Computational Social Science and Digital Humanities - Engineering <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…> Tutorials Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, which target specifically programmers with no prior knowledge of scientific python. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Developer Sprints A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. The conference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and receive tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Birds-of-a-Feather (BOF) Sessions Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. <https://github.com/scipy-conference/scipy-conference/blob/master/mailings/c…>Important Dates - March 14th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. - April 17th: Speakers selected - April 22nd: Sponsorship acceptance deadline - May 1st: Speaker schedule announced - May 6th, or 150 registrants: Early-bird registration ends - July 6-12th: 2 days of tutorials, 3 days of conference, 2 days of sprints We look forward to a very exciting conference and hope to see you all in Austin this summer! The SciPy2014 Organizers

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Re: GitHub now does diffs on rendered prose
by Johannes Schönberger 15 Feb '14

15 Feb '14

The only thing that's missing is the actual content :-) On Feb 14, 2014, at 18:51, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Wow, it's like the entire universe is aligning to help us write this paper! =D > > https://github.com/blog/1784-rendered-prose-diffs > > -- > 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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GitHub now does diffs on rendered prose
by Juan Nunez-Iglesias 14 Feb '14

14 Feb '14

Wow, it's like the entire universe is aligning to help us write this paper! =D https://github.com/blog/1784-rendered-prose-diffs

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Google Summer of Code 2014
by Stéfan van der Walt 13 Feb '14

13 Feb '14

Hi everyone If everything goes well, we'll be able to participate in this year's Google Summer of Code under the PSF umbrella. I've put up a page with ideas: https://github.com/scikit-image/scikit-image/wiki/GSoC-2014 Please have a look at it and edit as you see fit. Students, if you are interested in participating, now would be a great time to put in a few pull requests and to take part in conversations on the mailing list. Regards Stéfan

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io.Video hanging indefinitely on load
by !link 13 Feb '14

13 Feb '14

Hello, I'm trying to get skimage working with video, and I'm using a relatively small video to test the functionality I need. If I run the following code (with a video I know to play in multiple players) it seems to hang python. import os from skimage import io ** Message: pygobject_register_sinkfunc is deprecated (GstObject) video_path = os.path.join(os.getcwd(),'test.avi') data = io.Video(source = video_path) as in, I've let it run for 5 + min on a 2.5 MB file and had to kill the python process. I'm running OS X 10.9.1 and I have: Python 2.7.6 :: Anaconda 1.7.0 (x86_64) skimage 0.8.2 Gstreamer 1.2.3 from binary at http://gstreamer.freedesktop.org/ and gst-python010 installed In case it matters, I installed gst-python via: $ brew tap homebrew/versions $ brew install gst-python010 I would appreciate any suggestions or recommendations as to how to determine where the error is, and then how to go about correcting it.

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x,y coordinates of all the shape outlines
by Dan 11 Feb '14

11 Feb '14

Hi, I wish to get the x,y coordinates of all the shape outlines in this image http://break2012.weebly.com/uploads/1/3/5/8/13582971/682025_orig.gif Is it possible to do it using scikit-image? Thanks.

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Re: scikit-image paper
by Adam Hughes 11 Feb '14

11 Feb '14

Hey guys, I'm curious on your approach for introducing scikit image in the context of other available image processing libraries, without really stepping on anyone's toes so to speak. I'm referring to several image processing tools in a paper we're working on, and certainly would be interested in hearing your take on this issue. On Sun, Feb 9, 2014 at 6:37 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Hi all, > > 1. I'm unsure about writing the education or industry sections of the > paper, as I have little experience in either. I'm currently working on > another research example. I think we can have two, since it's *sci*kit-image! > Who worked on the Novice module? They might be a good candidate for the > Education section. And Neil might be your man for industry... =) > > 2. For stitching, some electron microscopy tiled images are another > alternative, see e.g.: http://www.ini.uzh.ch/~acardona/trakem2_manual.html > > 3. Big fan of PeerJ so let's get this show started! =) > > Juan. > > > > On Mon, Feb 10, 2014 at 6:39 AM, Jérôme Kieffer <google(a)terre-adelie.org>wrote: > >> On Sun, 9 Feb 2014 19:47:06 +0200 >> Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >> >> > On Sun, Feb 9, 2014 at 7:41 PM, Jérôme Kieffer <google(a)terre-adelie.org> >> wrote: >> > > I have plenty of panorama (already stitched) ... but raw images are >> > > available if you need for the publication. >> > > >> > > http://photo.terre-adelie.org/Panoramiques/html/dirindex.html >> > >> > That's awesome, thanks! We'll have a look through those and get in >> touch. >> > >> > Would it be acceptable to distribute the images freely with attribution? >> >> All those panorama (maybe there are 1 or 2 exceptions) have been >> assembled from images I took myself. I can specify a licence, probably >> CC-By it it fits you. Please take one without anybody on the image to >> avoid issues with what we call "droit à l'image" in French... (and >> doesn't exist in many counties: People appearing in content may have a >> right to control use of their image and to maintain their privacy.) >> http://fr.wikipedia.org/wiki/Droit_%C3%A0_l%27image >> >> Those panorama were assembled using gimp (before 2004) then with the help >> of >> Hugin. More recently I tested AutoPanoPro which is great while >> proprietary... >> >> Cheers, >> -- >> Jérôme Kieffer <google(a)terre-adelie.org> >> >> PS: I miss-used the word raw as they were all shout in JPEG mode. >> >> -- >> 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 a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/ReKcHGSaATU/unsubscribe. > To unsubscribe from this group and all of its topics, 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: scikit-image paper
by Jérôme Kieffer 09 Feb '14

09 Feb '14

On Sun, 9 Feb 2014 19:47:06 +0200 Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > On Sun, Feb 9, 2014 at 7:41 PM, Jérôme Kieffer <google(a)terre-adelie.org> wrote: > > I have plenty of panorama (already stitched) ... but raw images are > > available if you need for the publication. > > > > http://photo.terre-adelie.org/Panoramiques/html/dirindex.html > > That's awesome, thanks! We'll have a look through those and get in touch. > > Would it be acceptable to distribute the images freely with attribution? All those panorama (maybe there are 1 or 2 exceptions) have been assembled from images I took myself. I can specify a licence, probably CC-By it it fits you. Please take one without anybody on the image to avoid issues with what we call "droit à l'image" in French... (and doesn't exist in many counties: People appearing in content may have a right to control use of their image and to maintain their privacy.) http://fr.wikipedia.org/wiki/Droit_%C3%A0_l%27image Those panorama were assembled using gimp (before 2004) then with the help of Hugin. More recently I tested AutoPanoPro which is great while proprietary... Cheers, -- Jérôme Kieffer <google(a)terre-adelie.org> PS: I miss-used the word raw as they were all shout in JPEG mode.

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Re: incoherent face orientation in marching cubes
by Josh Warner 09 Feb '14

09 Feb '14

Calculate the gradient for each face, normalize it, and orient the face counterclockwise around the descent of said gradient vector. It would require some pretty heavy modification, but might be worth it. On the other hand, you could potentially hack in a fix (depends on how the STL package works) much easier by making the output double sided. A double-sided mesh has each face twice, covering both orientations This way you'd just append `faces` to itself, reverse indexing to flip the orientation of each face, e.g. ``` python import numpy as np from skimage.measure import marching_cubes verts, faces = marching_cubes(vol, value) faces = np.concatenate((faces, faces[:, -1], axis=0) # Remainder of STL export code for faces here ``` Which would be *far, far* simpler and less computationally intense than dealing with the gradients... Would you mind trying this quick fix, Janto? On Wednesday, January 8, 2014 6:35:28 PM UTC-6, Stefan van der Walt wrote: > > Josh, you said you had some ideas on how to add this--could you expand? >

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Re: scikit-image paper
by Johannes Schönberger 09 Feb '14

09 Feb '14

> This does look very appealing. I am sure we can hit that deadline > (Johannes is done with his section, mine is nearing completion and we > have two examples in the works). What other sections do we need? Introduction: Stefan Usage examples: Francois 1, Stefan 2 (?) Development practices: Johannes Roadmap: ??? (me?) Conclusion: (Stefan?)

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Re: Contribution to scikit-image
by Stéfan van der Walt 09 Feb '14

09 Feb '14

Hi Kakul On Sun, 09 Feb 2014 18:45:42 +0530, Kakul Chandra wrote: > I am a Computer Science undergraduate from Indian Institute of Technology > Roorkee. I am currently working on a project related to Text and Image > extraction from scanned Newspaper images.I am using scikit-image for that > purpose. I wanted to know I could contribute to scikit-image. We have a long list of bugs (some of them quite easy) that need to be fixed, so that would be one place to start. The other would be documentation. You can also look at our wiki at https://github.com/scikit-image/scikit-image in order to see a list of proposed future tasks. One feature I would like to see that is related to text is the stroke width transform. Regards StÃ©fan

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Contributing in Image Compression Algorithms
by MIT SHAH 09 Feb '14

09 Feb '14

Hi, I am working on Image Compression Algorithms. I want to contribute it in scikit-image. Can I contribute it ? I am asking this, because I didn't find Image Compression as Requested features on the following link : https://github.com/scikit-image/scikit-image/wiki/Requested-features Please guide me.

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