Mailman 3 February 2012 - scikit-image

Re: Imshow and Linescan - first version
by Guillaume Gay March 10, 2012

March 10, 2012

Le 26/02/2012 21:15, Stéfan van der Walt a écrit : > On Sat, Feb 25, 2012 at 11:10 AM, Tony Yu<tsyu80(a)gmail.com> wrote: >> Plugin system >> ------ >> It might be nice to have some sort of plugin system for the image viewer. >> That way, tools like this could be implemented a bit more easily and, also, >> easily added to the viewer or ignored by the user. > At the moment, we basically have a double-viewer implementation: > simply vs fancy. So we separate out > > imshow(x) and imshow(x, fancy=True) I thought one solution was to sub-class FigureCanvas, with extra buttons, but from what I understand, it is not that easy to do this at the platform independant level. But maybe adding arguments to the function call, for exemple imshow(x, set_contrast=True, linescan=True) plus keyboard toggles is enough? > >> agree to an extent. Nevertheless, I think providing a viewer that supplies >> *an infrastructure* for creating GUI tools might be really valuable. I >> haven't really thought through what this plugin system would look like, so >> it may just be a pipe dream. > This is a tricky problem (which set of tools to use, etc.)--but in > principle, it would be nice to have a few standard viewers, e.g., > image compare, image compare + parameter adjust, mask editor (to build > custom filters, e.g.) and image inspector (like the one you and > Guillaume are working on). > > Stéfan > What do you mean by mask editor? Something like a slider to adjust a threshold with a superimposed mask? Guillaume

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RFC: Multiple backends + speedy looping
by Stéfan van der Walt Feb. 29, 2012

Feb. 29, 2012

Hello everyone, After the skimage 0.5 release, it's time to start planning the Next Big Thing (TM). I hoped there would be a better solution by now, but it seems that one of our main weak points is still that we cannot do fast looping over images (e.g., filtering). We have multiple computing back-end support available as a pull request from Pieter Holtzhausen's GSOC--the code is fairly simple to understand, and doesn't complicate the framework more than necessary. This will allow us to, when doing convolutions e.g., first try doing it via OpenCL, and then to fall back to the CPU. We also have a full testing framework in place, so that the output from different back-ends are compared. Have a look at the code here: https://github.com/scikits-image/scikits-image/pull/14/files If you have a better solution or other alternatives in mind, please let me know; I'm keen to explore this space further. Regards Stéfan

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Re: [scikits-image] Restore previous io plugins (#152)
by Tony Yu Feb. 28, 2012

Feb. 28, 2012

2012/2/26 Stéfan van der Walt <stefan(a)sun.ac.za> > On Sun, Feb 26, 2012 at 12:25 PM, Christoph Gohlke <cjgohlke(a)gmail.com> > wrote: > > Instead of restoring the default plugins after each test module, maybe it > > would be better/cleaner/safer for the tests to never change the default > > plugins but to just load the plugin and explicitly specify the plugin in > > each imread, imwrite, etc. function call? It seems there is currently no > way > > to load a plugin without making it the default. This could be achieved by > > changing the use_plugin function to accept another option for the `kind` > > parameter, e.g. an empty string, signaling that the plugin should only be > > loaded. Probably too late for the 0.5 release. > > Ideally, the ``imread(..., plugin='fits')`` functionality should > auto-load the FITS-plugin---I should see why this is not currently > working, because it seems like a bug. > > Stéfan > I just submitted PR #157<https://github.com/scikits-image/scikits-image/pull/157> to address an error raised with non-loaded plugins. I'm not sure if this addresses the issue you mention above, but it's related, at least. -Tony

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Re: [scikits-image] Restore previous io plugins (#152)
by James Turner Feb. 27, 2012

Feb. 27, 2012

> Ideally, the ``imread(..., plugin='fits')`` functionality should > auto-load the FITS-plugin---I should see why this is not currently > working, because it seems like a bug. Oh, did someone say FITS plugin? I've been meaning to get back to that (sorry, too busy trying to finish up our Python distribution for astronomy). I believe I had some uncommitted changes after SciPy that we were pending me figuring out how to deal with metadata. I can try to look at this but it might take a couple of days to get to. Please let me know if you have Qs in the meantime (I'm not sure about auto-loading off the top of my head). Cheers, James.

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Windows binaries and 0.5
by Stéfan van der Walt Feb. 27, 2012

Feb. 27, 2012

Hey all, Christoph has already built scikits-image 0.5 packages for windows. Thanks a bunch, Chris! And thanks also to everyone who contributed to this release! Stéfan

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ANN: scikits-image v0.5
by Stéfan van der Walt Feb. 27, 2012

Feb. 27, 2012

Announcement: scikits-image 0.5 =============================== We're happy to announce the 0.5 release of scikits-image, our image processing toolbox for SciPy. For more information, please visit our website http://scikits-image.org New Features ------------ - Consistent intensity rescaling and improved range conversion. - Random walker segmentation. - Harris corner detection. - Otsu thresholding. - Block views, window views and montage. - Plugin for Christoph Golke's "tifffile". - Peak detection. - Improved FreeImage wrappers and meta-data reading. - 8-neighbor and background labelling. ... along with updates to the documentation and website, and a number of bug fixes. Contributors to this release ---------------------------- * Andreas Mueller * Brian Holt * Christoph Gohlke * Emmanuelle Gouillart * Michael Aye * Nelle Varoquaux * Nicolas Pinto * Nicolas Poilvert * Pieter Holtzhausen * Stefan van der Walt * Tony S Yu * Warren Weckesser * Zachary Pincus

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Re: [scikits-image] Restore previous io plugins (#152)
by Christoph Gohlke Feb. 27, 2012

Feb. 27, 2012

On 2/26/2012 12:05 PM, StÃ¯Â¿Â½fan van der Walt wrote: > On Sun, Feb 26, 2012 at 8:08 AM, Zachary Pincus<zachary.pincus(a)yale.edu> wrote: >>> This fixes an issue when running skimage.io.tests. When the tifffile plugin is left active two subsequent tests in skimage.morphology fail to read PNG files. >> Should I add similar teardown() stanzas to all of the image IO plugin tests so that none are left present thereafter, to avoid other such errors? (Though the other plugins read PNGs, it might be a better habit to tear everything down anyway.) > Thanks, I also thought this would be a good idea, after seeing > Christoph's patch. > > StÃ¯Â¿Â½fan > Instead of restoring the default plugins after each test module, maybe it would be better/cleaner/safer for the tests to never change the default plugins but to just load the plugin and explicitly specify the plugin in each imread, imwrite, etc. function call? It seems there is currently no way to load a plugin without making it the default. This could be achieved by changing the use_plugin function to accept another option for the `kind` parameter, e.g. an empty string, signaling that the plugin should only be loaded. Probably too late for the 0.5 release. Christoph

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Re: Imshow and Linescan - first version
by Stéfan van der Walt Feb. 26, 2012

Feb. 26, 2012

On Sat, Feb 25, 2012 at 11:10 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > Plugin system > ------ > It might be nice to have some sort of plugin system for the image viewer. > That way, tools like this could be implemented a bit more easily and, also, > easily added to the viewer or ignored by the user. At the moment, we basically have a double-viewer implementation: simply vs fancy. So we separate out imshow(x) and imshow(x, fancy=True) > agree to an extent. Nevertheless, I think providing a viewer that supplies > *an infrastructure* for creating GUI tools might be really valuable. I > haven't really thought through what this plugin system would look like, so > it may just be a pipe dream. This is a tricky problem (which set of tools to use, etc.)--but in principle, it would be nice to have a few standard viewers, e.g., image compare, image compare + parameter adjust, mask editor (to build custom filters, e.g.) and image inspector (like the one you and Guillaume are working on). Stéfan

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Re: 0.5 Release
by Christoph Gohlke Feb. 26, 2012

Feb. 26, 2012

On 2/25/2012 3:26 PM, StÃ¯Â¿Â½fan van der Walt wrote: > Hi all, > > I'm slightly behind on the release, but I have to cut it before PyData > this upcoming week, so if there's anything urgent that you'd like to > go in still, please let me know by tomorrow. I'll try to push out the > release Sunday evening, Pacific time. > > Thanks! > StÃ¯Â¿Â½fan > Hi StÃ¯Â¿Â½fan, I submitted a couple of pull requests, which fix all test errors and failures on win32 and win-amd64 platforms. Ciao, Christoph

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Re: [scikits-image] Restore previous io plugins (#152)
by Zachary Pincus Feb. 26, 2012

Feb. 26, 2012

Hi all, I see there's been a flurry of fixit and cleanup patches! Thanks all, especially Christoph, and especially as I see a lot of these oversights about python 3 syntax etc. came from my code. Sorry :) Thanks also for noticing the following issue Christoph: > This fixes an issue when running skimage.io.tests. When the tifffile plugin is left active two subsequent tests in skimage.morphology fail to read PNG files. Should I add similar teardown() stanzas to all of the image IO plugin tests so that none are left present thereafter, to avoid other such errors? (Though the other plugins read PNGs, it might be a better habit to tear everything down anyway.) Zach

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