[yt-dev] Default colormap

Matthew Turk matthewturk at gmail.com
Thu Jan 28 09:12:44 PST 2016


Thanks, Cameron.

Unless we get any other submissions, I've got a Google Form ready to go to
ask for preferences on this that I'll send out tomorrow morning.  It
includes the montages and color space diagrams; they can all be viewed
here: https://drive.google.com/open?id=0B1DaRHnSGW8Za0U4cEFTTzVPcVE

-Matt

On Wed, Jan 27, 2016 at 10:22 PM, Cameron Hummels <chummels at gmail.com>
wrote:

> I'd like to propose this colormap:
>
> http://i.imgur.com/nKFZWSC.png
>
> Script here:
>
> http://paste.yt-project.org/show/6194/
>
> Cameron
>
> On Thu, Jan 21, 2016 at 11:05 AM, Matthew Turk <matthewturk at gmail.com>
> wrote:
>
>> Sounds good, but before we do that, I think we should have a suitable
>> waiting period for others to propose them.  I'll send an email out to
>> yt-users asking for ideas on it.
>>
>> On Thu, Jan 21, 2016 at 12:10 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> I think we should probably put it up for a vote and we should send an
>>> e-mail to yt-users about it.
>>>
>>> On Thu, Jan 21, 2016 at 12:06 PM, Matthew Turk <matthewturk at gmail.com>
>>> wrote:
>>>
>>>> Hi folks,
>>>>
>>>> I've put up a comparison image:
>>>>
>>>> http://i.imgur.com/Afxdb0G.jpg
>>>>
>>>> Left is Kacper, middle is me, right is Nathan.
>>>>
>>>> Honestly I think all could go in, but we should pick a default --
>>>> whether it's one of these or a different one.  Anyone have a strong opinion?
>>>>
>>>> -Matt
>>>>
>>>> On Mon, Jan 18, 2016 at 10:19 AM, B.W. Keller <kellerbw at mcmaster.ca>
>>>> wrote:
>>>>
>>>>> Wow, all of these look great.  I think I like Matt's best for painting
>>>>> our bikeshed, but I would be happy with any of them.
>>>>>
>>>>> On Mon, Jan 18, 2016 at 11:10 AM, Kacper Kowalik <
>>>>> xarthisius.kk at gmail.com> wrote:
>>>>>
>>>>>> On 01/18/2016 09:45 AM, Matthew Turk wrote:
>>>>>> > Hi all,
>>>>>> >
>>>>>> > I've experimented a bit and come up with this:
>>>>>> >
>>>>>> > https://images.hub.yt/u/fido/m/9bbe3cf6-png/
>>>>>> >
>>>>>> > The script:
>>>>>> >
>>>>>> > http://paste.yt-project.org/show/6151/
>>>>>> >
>>>>>> > This was designed with the viscm project, which is awfully cool.
>>>>>> What
>>>>>> > do folks think?  I think Kacper and Nathan also experimented with
>>>>>> > viscm and have some ideas too, so maybe we should put it up for an
>>>>>> > eventual vote.
>>>>>>
>>>>>> This is my experiment:
>>>>>>
>>>>>> https://images.hub.yt/u/fido/m/f180a901-png/
>>>>>>
>>>>>> Source:
>>>>>>
>>>>>> http://paste.yt-project.org/show/6166/
>>>>>>
>>>>>> Cheers,
>>>>>> Kacper
>>>>>>
>>>>>>
>>>>>> >
>>>>>> > Also, I would campaign for calling whatever our new colormap turns
>>>>>> out
>>>>>> > to be one of these three things, in increasing order of my
>>>>>> preference:
>>>>>> >
>>>>>> > agar
>>>>>> > kelp
>>>>>> > kanten
>>>>>> >
>>>>>> > -Matt
>>>>>> >
>>>>>> > On Thu, Jan 14, 2016 at 10:57 AM, Matthew Turk <
>>>>>> matthewturk at gmail.com> wrote:
>>>>>> >> Hi Stuart and everyone else,
>>>>>> >>
>>>>>> >> This is great info.  I appreciate everyone's thoughtful replies.
>>>>>> >>
>>>>>> >> Having both a sequential colormap (which would replace algae) and a
>>>>>> >> diverging colormap, would be awesome.  The Paraview devs shipped
>>>>>> the
>>>>>> >> new matplotlib ones (like Inferno) in 5.0.  I think it would be a
>>>>>> fun
>>>>>> >> experiment to see if we can come up with something sufficiently
>>>>>> >> "branded" or different.  And then if we can't, fall back on
>>>>>> something
>>>>>> >> like Inferno?
>>>>>> >>
>>>>>> >> -Matt
>>>>>> >>
>>>>>> >> On Wed, Jan 6, 2016 at 12:48 PM, Levy, Stuart A <
>>>>>> salevy at illinois.edu> wrote:
>>>>>> >>> There was a fair bit of discussion about colormaps - terrible,
>>>>>> useful,
>>>>>> >>> beautiful - at IEEE Vis last October.   The viridis colormap was
>>>>>> a featured
>>>>>> >>> one.   So was the traditional rainbow, which lots of info-vis and
>>>>>> perceptual
>>>>>> >>> people piled on to criticize.
>>>>>> >>>
>>>>>> >>> Among design criteria for a continuous-valued colormap is whether
>>>>>> it's
>>>>>> >>> "sequential" (like the typical yt colormap, or viridis) or
>>>>>> "diverging".
>>>>>> >>> You'd want a diverging colormap to show signed deviations from a
>>>>>> norm -
>>>>>> >>> where the eye should be caught by places where a value is either
>>>>>> much less
>>>>>> >>> than, or much more than, something in the middle.   Is it worth
>>>>>> offering a
>>>>>> >>> typical divergent colormap, as well as a new typical sequential
>>>>>> one, in yt?
>>>>>> >>>
>>>>>> >>> Note that among the Stefan van der Walt & Nathaniel Smith writeup
>>>>>> (
>>>>>> >>> http://bids.github.io/colormap/ ) on their development of better
>>>>>> cmaps, they
>>>>>> >>> use Nathan Goldbaum's galaxy evolution as a test case for six
>>>>>> (sequential)
>>>>>> >>> examples! =>
>>>>>> http://vorpus.org/~njs/goldbaum-galaxies-all-colormaps.mkv
>>>>>> >>>
>>>>>> >>> A neat web site with sample colormaps - aimed at mapping discrete
>>>>>> values on
>>>>>> >>> geographic maps, so not directly applicable but cool - is this,
>>>>>> by Cynthia
>>>>>> >>> Brewer and Mark Harrower at PSU:
>>>>>> >>>     http://colorbrewer2.org/
>>>>>> >>> It has a library of predesigned cmaps, and lets you sift them by
>>>>>> being
>>>>>> >>> colorblind-safe, photocopy safe, etc.
>>>>>> >>> ________________________________
>>>>>> >>> From: yt-dev [yt-dev-bounces at lists.spacepope.org] on behalf of
>>>>>> B.W. Keller
>>>>>> >>> [kellerbw at mcmaster.ca]
>>>>>> >>> Sent: Wednesday, January 06, 2016 12:13
>>>>>> >>> To: yt-dev at lists.spacepope.org
>>>>>> >>> Subject: Re: [yt-dev] Default colormap
>>>>>> >>>
>>>>>> >>> There is a really excellent paper on designing color maps called
>>>>>> "Color
>>>>>> >>> Sequences for Univariate Maps: Theory, Experiments, and
>>>>>> Principles" that you
>>>>>> >>> can get here:
>>>>>> >>>
>>>>>> http://ccom.unh.edu/sites/default/files/publications/Ware_1988_CGA_Color_sequences_univariate_maps.pdf
>>>>>> >>>
>>>>>> >>> If we design a new colormap, this would be a good reference along
>>>>>> with those
>>>>>> >>> scipy resources.  I personally would love to have an accessible,
>>>>>> yt-custom
>>>>>> >>> colormap.
>>>>>> >>>
>>>>>> >>> On Wed, Jan 6, 2016 at 11:50 AM, Erik Schnetter <
>>>>>> schnetter at gmail.com> wrote:
>>>>>> >>>>
>>>>>> >>>> I think there are several colourmaps that were created when
>>>>>> Viridis
>>>>>> >>>> was invented. I personally like Inferno.
>>>>>> >>>>
>>>>>> >>>> -erik
>>>>>> >>>>
>>>>>> >>>> On Wed, Jan 6, 2016 at 11:34 AM, Nathan Goldbaum <
>>>>>> nathan12343 at gmail.com>
>>>>>> >>>> wrote:
>>>>>> >>>>> I would also be for coming up with our own colormap. That said,
>>>>>> I think
>>>>>> >>>>> simply modifying algae won't be enough, since it is too
>>>>>> perceptually
>>>>>> >>>>> nonlinear.
>>>>>> >>>>>
>>>>>> >>>>> On Wed, Jan 6, 2016 at 10:32 AM, John ZuHone <jzuhone at gmail.com>
>>>>>> wrote:
>>>>>> >>>>>>
>>>>>> >>>>>> I would go for modifying algae.
>>>>>> >>>>>>
>>>>>> >>>>>>> On Jan 6, 2016, at 11:30 AM, Matthew Turk <
>>>>>> matthewturk at gmail.com>
>>>>>> >>>>>>> wrote:
>>>>>> >>>>>>>
>>>>>> >>>>>>> Hi folks,
>>>>>> >>>>>>>
>>>>>> >>>>>>> For a long time we've used "algae," which was designed by
>>>>>> Britton
>>>>>> >>>>>>> about eight years ago, as the default colormap.  This has
>>>>>> been really
>>>>>> >>>>>>> nice for "branding" yt -- if you see an algae plot, it's
>>>>>> probably
>>>>>> >>>>>>> (not
>>>>>> >>>>>>> definitely) made with yt.  But it's also not accessible from a
>>>>>> >>>>>>> colorblindness perspective.  Stefan van der Walt has been
>>>>>> giving some
>>>>>> >>>>>>> really great talks lately about building a better colormap for
>>>>>> >>>>>>> matplotlib (e.g., https://www.youtube.com/watch?v=xAoljeRJ3lU
>>>>>> ) which
>>>>>> >>>>>>> culminated in viridis, which is shipping in recent versions of
>>>>>> >>>>>>> matplotlib and will become the default.
>>>>>> >>>>>>>
>>>>>> >>>>>>> In support of this, he built a tool called viscm which can
>>>>>> generate
>>>>>> >>>>>>> reduced versions of colormaps to show what they would be like
>>>>>> with
>>>>>> >>>>>>> varying degrees of insensitivity to color.  I've generated
>>>>>> outputs
>>>>>> >>>>>>> from viscm of three of the custom colormaps we ship with yt:
>>>>>> >>>>>>>
>>>>>> >>>>>>> Algae: https://images.hub.yt/u/fido/m/d275d5e1-png/
>>>>>> >>>>>>> Cubehelix: https://images.hub.yt/u/fido/m/8e698928-png/ (I
>>>>>> believe
>>>>>> >>>>>>> this is now also shipped with MPL)
>>>>>> >>>>>>> Kamae: https://images.hub.yt/u/fido/m/e0e40efa-png/
>>>>>> >>>>>>>
>>>>>> >>>>>>> I love algae, but it's not the best from an accessibility
>>>>>> >>>>>>> perspective.
>>>>>> >>>>>>>
>>>>>> >>>>>>> I'd like to propose that we use a new default colormap.  If
>>>>>> we do
>>>>>> >>>>>>> this, I see two options:
>>>>>> >>>>>>>
>>>>>> >>>>>>> * Retain a "branding" by developing a new one either by using
>>>>>> the
>>>>>> >>>>>>> techniques used by matplotlib (or one of the maps they opted
>>>>>> not to
>>>>>> >>>>>>> use) or by modifying algae to be more accessible; looking at
>>>>>> the
>>>>>> >>>>>>> response functions, I suspect it would be reasonably possible
>>>>>> to
>>>>>> >>>>>>> modify it.  (Modifying algae is my preference.)
>>>>>> >>>>>>> * Use viridis (which we may then have to ship if we have older
>>>>>> >>>>>>> versions of matplotlib to support)
>>>>>> >>>>>>>
>>>>>> >>>>>>> -Matt
>>>>>> >>>>>>> _______________________________________________
>>>>>> >>>>>>> yt-dev mailing list
>>>>>> >>>>>>> yt-dev at lists.spacepope.org
>>>>>> >>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>>>>>> >>>>>>
>>>>>> >>>>>> _______________________________________________
>>>>>> >>>>>> yt-dev mailing list
>>>>>> >>>>>> yt-dev at lists.spacepope.org
>>>>>> >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> _______________________________________________
>>>>>> >>>>> yt-dev mailing list
>>>>>> >>>>> yt-dev at lists.spacepope.org
>>>>>> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>>>>>> >>>>>
>>>>>> >>>>
>>>>>> >>>>
>>>>>> >>>>
>>>>>> >>>> --
>>>>>> >>>> Erik Schnetter <schnetter at gmail.com>
>>>>>> >>>> http://www.perimeterinstitute.ca/personal/eschnetter/
>>>>>> >>>> _______________________________________________
>>>>>> >>>> yt-dev mailing list
>>>>>> >>>> yt-dev at lists.spacepope.org
>>>>>> >>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>>>>>> >>>
>>>>>> >>>
>>>>>> >>>
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>>>>>> >
>>>>>>
>>>>>>
>>>>>>
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>>>>>>
>>>>>
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>
>
> --
> Cameron Hummels
> NSF Postdoctoral Fellow
> Department of Astronomy
> California Institute of Technology
> http://chummels.org
>
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