Mailman 3 December 2014 - scikit-image

Local GLCM features
by Willem Olding 09 Dec '14

09 Dec '14

Hi, The scikit-image implementation of GLCM computes the grey level co-occurrence matrix for entire images or image patches. For some image labeling problems it is preferred to calculate GLCM features for each individual pixel using a sliding window approach as described in http://www.fp.ucalgary.ca/mhallbey/texture_calculations.htm. This approach can be implemented in scikit-image using a combination of view_as_windows, greycomatrix and greycoprops although I found it to be too slow for practical use. To overcome this I extended scikit-image with a function that performs the sliding window as fast cython code. It takes an image, distance, angle and window size and generates a texture image with the GLCM features ['mean','variance','contrast','dissimilarity','homogeneity','ASM','entropy','correlation'] calculated at every pixel. Would this be something people are interested in including as part of scikit-image? Regards, Willem

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Re: How do you keep documentation so nice?
by Stefan van der Walt 09 Dec '14

09 Dec '14

Hi Adam On 2014-12-09 22:54:34, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Nevermind guys, I was able to get it working through that sphinx-gallery > link that Stefan set. I'm not sure how--that repo still looks to be fairly empty! The process is: we run tools that generates .rst files, the rst files get compiled by Sphinx, during which the plots etc. get generated. The result is then pushed to a repository on GitHub. Easiest way to understand it is to run the script and examine the new files created. Stéfan

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Permalinks embedded on mailing list messages
by Juan Nunez-Iglesias 09 Dec '14

09 Dec '14

Does anyone know of a way to get these? My current workflow involves Googling for the skimage mailing list, finding the right link (it's not the top hit), hunting down the right message, and then two clicks and a copy-paste to get the link. Nabble provides them by default (much as GitHub does), and they are very useful, since mailing list messages are often quite shareable. I'd even advocate moving to Nabble if there's no way to do this.

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Re: Travis-wheels fix?
by Steven Silvester 09 Dec '14

09 Dec '14

I think I know what to do: this line in `travis_setup.py` is causing it to fail on retry: `sh -e /etc/init.d/xvfb start` I'll try moving that to `.travis.yml` and see if that clears it up. On Tue, Dec 9, 2014 at 3:39 PM, Matthew Brett <matthew.brett(a)gmail.com> wrote: > I wonder if the directory listing is the problem? Maybe we could try the > latest github pip with the retry option? > > -- > 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/hCKQU-PSasM/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

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Re: Travis-wheels fix?
by Matthew Brett 09 Dec '14

09 Dec '14

I wonder if the directory listing is the problem? Maybe we could try the latest github pip with the retry option?

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Re: How do you keep documentation so nice?
by Adam Hughes 09 Dec '14

09 Dec '14

Nevermind guys, I was able to get it working through that sphinx-gallery link that Stefan set. Thanks for all of your help! Really feels great to see how nice a website can be created from just auto-docs. On Tue, Dec 9, 2014 at 2:58 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > PS, > > Tony, I don't see an index.rst file in scikit-images gallery. You're > talking about this folder, yes?: > > https://github.com/scikit-image/scikit-image/tree/master/doc/examples > > On Tue, Dec 9, 2014 at 2:57 PM, Adam Hughes <hughesadam87(a)gmail.com> > wrote: > >> Thanks Tony and Stefan for the resources, I will start working on them >> now. >> >> On Tue, Dec 9, 2014 at 11:58 AM, Stefan van der Walt <stefan(a)sun.ac.za> >> wrote: >> >>> Hi Adam >>> >>> On 2014-12-09 04:12:17, Tony Yu <tsyu80(a)gmail.com> wrote: >>> >> I really am impressed by this plt2rst.py module for autogenerating >>> example >>> >> documentation! >>> >>> Also have a look at this project, which tries to unify the gallery >>> builders of the different projects: >>> >>> https://github.com/sphinx-gallery/sphinx-gallery >>> >>> 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/k5K6_vanZVI/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> scikit-image+unsubscribe(a)googlegroups.com. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >

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Re: How do you keep documentation so nice?
by Adam Hughes 09 Dec '14

09 Dec '14

PS, Tony, I don't see an index.rst file in scikit-images gallery. You're talking about this folder, yes?: https://github.com/scikit-image/scikit-image/tree/master/doc/examples On Tue, Dec 9, 2014 at 2:57 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Thanks Tony and Stefan for the resources, I will start working on them now. > > On Tue, Dec 9, 2014 at 11:58 AM, Stefan van der Walt <stefan(a)sun.ac.za> > wrote: > >> Hi Adam >> >> On 2014-12-09 04:12:17, Tony Yu <tsyu80(a)gmail.com> wrote: >> >> I really am impressed by this plt2rst.py module for autogenerating >> example >> >> documentation! >> >> Also have a look at this project, which tries to unify the gallery >> builders of the different projects: >> >> https://github.com/sphinx-gallery/sphinx-gallery >> >> 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/k5K6_vanZVI/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > >

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Re: How do you keep documentation so nice?
by Stefan van der Walt 09 Dec '14

09 Dec '14

Hi Adam On 2014-12-09 04:12:17, Tony Yu <tsyu80(a)gmail.com> wrote: >> I really am impressed by this plt2rst.py module for autogenerating example >> documentation! Also have a look at this project, which tries to unify the gallery builders of the different projects: https://github.com/sphinx-gallery/sphinx-gallery Stéfan

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Re: How do you keep documentation so nice?
by Tony Yu 08 Dec '14

08 Dec '14

Hi Adam! On Mon, Dec 8, 2014 at 5:40 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > I really am impressed by this plt2rst.py module for autogenerating example > documentation! > > I've been trying to implement it just to test it out and think I have it > setup right in terms of placement in my docs directory, I made an example > plot_test.py file in examples, but I'm confused on how to actually use the > plt2rst.py module. Consider this line from that file: > > def setup(app): > app.connect('builder-inited', generate_example_galleries) > > app.add_config_value('plot2rst_paths', > ('../examples', 'auto_examples'), True > > When/how is this ever called? The examples themselves don't use these > directives; so when is this found? > This plotting code is partially my fault, so I'll try to explain based on memory. I should say, though, that I adapted this code from an older version in the `scikit-image` docs, which took it from `scikit-learn` (which may have taken it from nipy or some other project). That is to say, I don't completely understand all the things. ;) This particular `setup(app)` function is run as part of the Sphinx infrastructure (see http://sphinx-doc.org/extdev/tutorial.html). > When I build in my make file, no auto_examples.html file is ever created > in my build directory. So I'm thinking I'm not using this correctly. Is > there another step besides just doing make build? > There's a bit of documentation written up here: https://github.com/tonysyu/mpltools/blob/master/doc/source/getting_started.… One possible hang-up is that examples are expected to start with `plot_` and an `index.rst` file is required in gallery directories. I haven't looked at this in a while, but if you have any more questions, I can try to dig into the code a bit to try to remember what's going on. Cheers! -Tony

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Re: How do you keep documentation so nice?
by Adam Hughes 08 Dec '14

08 Dec '14

I really am impressed by this plt2rst.py module for autogenerating example documentation! I've been trying to implement it just to test it out and think I have it setup right in terms of placement in my docs directory, I made an example plot_test.py file in examples, but I'm confused on how to actually use the plt2rst.py module. Consider this line from that file: def setup(app): app.connect('builder-inited', generate_example_galleries) app.add_config_value('plot2rst_paths', ('../examples', 'auto_examples'), True When/how is this ever called? The examples themselves don't use these directives; so when is this found? When I build in my make file, no auto_examples.html file is ever created in my build directory. So I'm thinking I'm not using this correctly. Is there another step besides just doing make build? On Sun, Dec 7, 2014 at 7:22 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Thanks Juan. It's funny, but I feel like writing documents is 10 times > harder than writing software > > On Sun, Dec 7, 2014 at 7:17 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> > wrote: > >> Hahaha it's not that dumb! I personally have tried to dive into the doc >> build process a few times but have found it quite opaque, so I wouldn't >> mind if Stéfan and/or Tony elaborated a bit here about the build system! =) >> >> But as to drawing inspiration, I'm pretty sure it's all BSD, which means >> you can draw even a bit more than that! =) >> >> >> >> >> On Mon, Dec 8, 2014 at 11:14 AM, Adam Hughes <hughesadam87(a)gmail.com> >> wrote: >> >>> I'm dumb. It's clearly right there on your github page in "docs". >>> Geez. >>> >>> It's ok if I draw inspiration from you guys, right? >>> >>> On Sun, Dec 7, 2014 at 7:11 PM, Adam Hughes <hughesadam87(a)gmail.com> >>> wrote: >>> >>>> Hi, >>>> >>>> I've been working with sphinx api-doc for autogenerating some >>>> documentation for a package, and the output is a farcry from the nice, >>>> super-slick layout that scikit-image has. I saw that on the bottom of your >>>> page, the docs are built with sphinx and bootstrap. Is the source code for >>>> the documentation available for perusing by chance? I'd love to get some >>>> insights on how you keep your page so nice and tidy! >>>> >>>> -- >>>> 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/k5K6_vanZVI/unsubscribe. >>>> To unsubscribe from this group and all its topics, send an email to >>>> scikit-image+unsubscribe(a)googlegroups.com. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> 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/d/optout. >>> >> >> -- >> 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/k5K6_vanZVI/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > >

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