Mailman 3 February 2014 - scikit-image

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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