Mailman 3 March 2015 - scikit-image

Fwd: ANN: SciPy (Scientific Python) 2015 Call for Proposals & Registration Open - tutorial & talk submissions due April 1st
by Nelle Varoquaux 25 Mar '15

25 Mar '15

Hello everyone, (I apologize for the cross posting). This is a quick reminder that the call for submission for Scipy 2015 is open but due April 1st! There is only 7 days left to submit a proposal. Thanks, Nelle ---------- Forwarded message ---------- From: Courtenay Godshall <cgodshall(a)enthought.com> Date: 19 March 2015 at 04:46 Subject: ANN: SciPy (Scientific Python) 2015 Call for Proposals & Registration Open - tutorial & talk submissions due April 1st To: python-list(a)python.org **SciPy 2015 Conference (Scientific Computing with Python) Call for Proposals: Submit Your Tutorial and Talk Ideas by April 1, 2015 at http://scipy2015.scipy.org.** SciPy 2015, the fourteenth annual Scientific Computing with Python conference, will be held July 6-12, 2015 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 brings together over 500 participants from industry, academia, and government to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. 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. More info available on the conference website at http://scipy2015.scipy.org; you can also sign up on the website for mailing list updates or follow @scipyconf on Twitter. We hope you'll join us - early bird registration is open until May 15, 2015 at http://scipy2015.scipy.org/ehome/115969/259272/?& We encourage you to submit tutorial or talk proposals in the categories below; please also share with others who you'd like to see participate! Submit via the conference website @ http://scipy2015.scipy.org. *SCIPY TUTORIAL SESSION PROPOSALS - DEADLINE EXTENDED TO WED APRIL 1, 2015* The SciPy experience kicks off with two days of tutorials. These sessions provide extremely affordable access to expert training, and consistently receive fantastic feedback from participants. We're looking for submissions on topics from introductory to advanced - we'll have attendees across the gamut looking to learn. Whether you are a major contributor to a scientific Python library or an expert-level user, this is a great opportunity to share your knowledge and stipends are available. Submit Your Tutorial Proposal on the SciPy 2015 website: http://scipy2015.scipy.org *SCIPY TALK AND POSTER SUBMISSIONS - DUE April 1, 2015* SciPy 2015 will include 3 major topic tracks and 7 mini-symposia tracks. Submit Your Talk Proposal on the SciPy 2015 website: http://scipy2015.scipy.org Major topic tracks include: - Scientific Computing in Python (General track) - Python in Data Science - Quantitative and Computational Social Sciences Mini-symposia will include the applications of Python in: - Astronomy and astrophysics - Computational life and medical sciences - Engineering - Geographic information systems (GIS) - Geophysics - Oceanography and meteorology - Visualization, vision and imaging If you have any questions or comments, feel free to contact us at: scipy-organizers(a)scipy.org. -- https://mail.python.org/mailman/listinfo/python-list

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Re: GSoC: Rewriting scipy.ndimage in Cython
by Ralf Gommers 25 Mar '15

25 Mar '15

On Wed, Mar 25, 2015 at 4:26 AM, Jaime Fernández del Río < jaime.frio(a)gmail.com> wrote: > On Tue, Mar 24, 2015 at 5:34 PM, AMAN singh <ug201310004(a)iitj.ac.in> > wrote: > >> Hi Everyone >> >> I have made a basic draft of my proposal here >> <https://docs.google.com/document/d/1-dRqhFzyWnoDJl82KsYECo00B82osR6hujaZ008…> >> . >> Please review it and suggest modifications. >> > > Hi Aman, > > This may not be 100% true for all the functionality, but I believe that > the gist of the ndimage module is in the 4-5 object-like constructs in > ni_support, namely: > > > - NI_Iterator in its three flavors: point, subspace and line iterator, > - NI_LineBuffer and > - NI_FilterIterator. > > Closely linked to this is the choice of a method to deal with multiple > dtypes, a question for which I don't think there is an obvious answer. > Since performance is critical, you may want to take a look at bottleneck's > use of templates that are pre-processed before cythonizing and compiling. > > If you get these right, then rather than the leaves of the tree, you will > have built a solid foundation, more like the the trunk: porting all the > other modules is then going to mostly be little more than an exercise in > translation. So I would suggest that you devote more time to getting these > fundamental questions right, as some trial and error is going to be > inevitable. > This sounds like great advice. Comments on the timeline: - week 1 "reading through the code": I think you should cover, and will have covered this, in the communitiy bonding period. At the start of week 1 you should be at the point where you start tacking the problem. Probably by doing what Jaime says above. - unit tests, docs and benchmarks: these cannot be separated from writing code. Each PR should have decent unit test coverage and a decent docstring. Plus since performance is critical you have to benchmark your code as you go. The only thing you could reserve time for at the end is writing some longer documentation (maybe a tutorial), benchmarks in ASV format (see https://github.com/scipy/scipy/tree/master/benchmarks) and some minor cleanups. Regarding "I will also use better algorithms when possible to improve the time complexity of the functions": it is important to not mix porting code from C to Cython with changing the algorithm, because when output of a function doesn't match the current Scipy output you don't know whether porting or algorithm changes are the cause. Cheers, Ralf

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Fiscal sponsorship
by Stefan van der Walt 24 Mar '15

24 Mar '15

Hi everyone scikit-image is getting enough traction that we can consider finding some development sponsorships (think, e.g., of getting the team together for sprints, etc.). Along that vein, I would like to propose that we sign a fiscal sponsorship agreement with NumFocus to manage the legal aspects of any funds raised. Please let me know if you have any concerns. Regards Stéfan

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Range of a,b in Lab color space
by Dzung Nguyen 24 Mar '15

24 Mar '15

What is the range of a, b coordinate in Lab space?

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Re: Water-shedding non-circular particles
by Emmanuelle Gouillart 24 Mar '15

24 Mar '15

Hi Clay, how do you select the markers and the elevation function used in the watershed algorithm? Could you include the code that results in the segmentation you attached? Cheers, Emmanuelle On Thu, Mar 19, 2015 at 06:07:57PM -0400, Claiborne Morton wrote: > Hey guys, Im still having trouble finding ways to separate touching particles > if the are not both circular. Further when dealing with elliptical shapes, a > single particle tends to incorrectly get cut in half. Any ideas how I could > change parameters in the water-shedding function to correct for this? Attached > are a few problem cases so you can see examples. > Thanks, > Clay > Inline image 1

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Re: Dynamic intensity scaling for CollectionViewer
by Ferdinand Greiss 24 Mar '15

24 Mar '15

from skimage.viewer import CollectionViewer from skimage.viewer.plugins.lineprofile import LineProfile import numpy as np stack = np.random.randn(100, 50, 50) stack *= np.exp(-0.1*np.arange(stack.shape[0]))[:, np.newaxis, np.newaxis] viewer = CollectionViewer(stack) viewer += LineProfile() viewer.show() I actually did change the source code of tifffile.py written by Christoph Gohlke on line 4660 to include rescaling for min and max of current image in image stack (by pressing r). But it'd be nice to still be able to use your plugins... Thanks for your prompt answer... Ferdinand Am Montag, 23. März 2015 23:57:11 UTC+1 schrieb stefanv: > > Hi Ferdinand > > On Mon, Mar 23, 2015 at 8:15 AM, Ferdinand Greiss > <ferdinan...(a)gmail.com <javascript:>> wrote: > > I was wondering whether it would be straight forward to implement > automatic > > rescaling of intensity (or y axis on LineProfile widget) in order to > account > > for bleaching in image sequences. Otherwise the line plot will vanish > below > > the pre-computed value of the first image and I won't be able to see > much > > after the first few images. > > I think that should be pretty simple. Can you share a code snippet of > how you are using it currently? > > Stéfan >

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Dynamic intensity scaling for CollectionViewer
by Ferdinand Greiss 23 Mar '15

23 Mar '15

Hallo, Thanks for your amazing project on image processing. I was wondering whether it would be straight forward to implement automatic rescaling of intensity (or y axis on LineProfile widget) in order to account for bleaching in image sequences. Otherwise the line plot will vanish below the pre-computed value of the first image and I won't be able to see much after the first few images. Thanks for any help or/and suggestions. Ferdinand

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SpaceX public photo archive
by Stefan van der Walt 23 Mar '15

23 Mar '15

Hi everyone A heads up from Josh Warner on Gitter that SpaceX now has an enormous photo collection in the public domain: https://www.flickr.com/photos/spacexphotos Stéfan

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Light Exhibit
by Stefan van der Walt 23 Mar '15

23 Mar '15

Hi everyone Here's a call for participation in an image exhibition taking place in Paris and San Francisco, among others. """ Light in all of its forms allows us to communicate, entertain, explore, and understand the world we inhabit and the Universe we live in. This exhibit shows you some examples of the myriad of wonderful things that light can do, and how it plays a critical role in our lives every day. WE ARE LOOKING FOR IMAGES THAT: -Illustrate different aspects/phenomena of light in nature, such as lensing, reflection, refraction, atomic collisions, shadows, etc. Examples might include sunsets showing a distorted Sun, auroras, rainbows, sunrises, light rays, lightning, Sun halos, moon dogs, etc. -We are also looking for natural photos of biologic importance tied to light such as sea turtle hatchlings, migrating birds, butterflies, bats at dusk, photosynthesis, sunflowers, etc. -Microscopic images and medically-themed images such as brain scans, images of cells, etc. -Also needed, Earth at Night scences, including our views of the Milky Way at night, "light pollution" themed images, etc. -We have pinned examples to Pinterest: - http://www.pinterest.com/kimberlyarcand/light-beyond-the-bulb-core-30%2B-im… """ http://lightexhibit.org/about.html Stéfan

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Re: GSoC: Rewriting scipy.ndimage in Cython
by Stéfan van der Walt 23 Mar '15

23 Mar '15

Hi folks, On Sun, Mar 15, 2015 at 10:45 AM, Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > @all: it's maybe good to know that Aman has already submitted 5 PRs to Scipy > (4 small ones merged, 1 larger one for which the bottleneck is on our side): > https://github.com/scipy/scipy/pulls?q=is%3Apr+author%3Abewithaman+is%3Aclo… I wasn't aware--thanks for the heads-up! Stéfan

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