Since I am deconstructing the rainbow/spectrum in RGB, HSV color spaces, I will show it in dichromat “color space”, and finally will then make a new one in CIE L*a*b* color space I thought I should include a review of the basics. So what is a color space? This good post answers that question.
This is the first post in a series on the rainbow and similar color palettes. My goal is to demonstrate it is not a good idea to use these palettes to display scientific data, and then answer these two questions: (1) is there anything we can do to “fix” the rainbow, and (2) if not, can we design a new one from scratch.
In a previous post I showed a pseudo-3D rendering of my left hand x-ray using intensity (which is a measure of bone thickness) as the elevation. I mapped the rendering to both grayscale and rainbow color palettes, and here I reproduced the two images side by side:
I used this example to argue (briefly) that the rainbow obscures some details and confuses images by introducing artifacts. Notice that in this case it clearly reduces the effectiveness of the pseudo-3D rendering in general. It also introduces inversions in the perception of elevation. The thick part in the head of the radius bone, indicated by the arrow, looks like a depression, whereas it is clearly (and correctly) a high in the grayscale version.
Before starting my series on perceptual color palettes I thought it was worth mentioning an excellent function I found some time ago on the Matlab File Exchange. The function is called Light and Bartlein Color Maps. It was a Matlab Pick of the week, and it can be used to create four color palettes discussed in the EOS paper by Light and Bartlein. Each of these palettes is suited for a specific task, and the authors claim they are non confusing for viewers with color vision deficiencies.
In the remainder of this post I will showcase one of the palettes, called orange-white-purple, as it is good divergent scheme [1]. With the code below I am going to load the World Topography Matlab demo data, create the palette and use it to display the data.
%% load World Topography Matlab demo
load topo;
%% create Light Bartlein orange-white-purple diverging scheme
LB=flipud(lbmap(256,'BrownBlue')); % flip it so blue is for negative(ocean)
% and green for positive (land)
%% plot map
fig2 = figure;
imagesc(flipud(topo));
axis equal
axis tight
axis off
set(fig2,'Position',[720 400 980 580]);
title(' Non-symmetric divergent orange-white-purple palette','Color',...
'k','FontSize',12,'FontWeight','demi');
colormap(LB);
colorbar;
And here is the result below. I like this color scheme better than many othera for divergent data. One only issue in the figure, although not inherently due to the palette itself [2], is that the centre of the palette is not at the zero. This is a problem since the zero is such an important element in ratio data, in this case representing sea level.
The problem fortunately can be easily fixed by clipping the data limit to a symmetric range. In Matlab this has to be done programmatically, and rather than going about it with trial and error I like to do it automatically with the code below:
Stephen Westland of Colour chat recently posted about a clever new LED traffic light developed in Japan. Here’s my tweet with the link to Westland’s original blog post:
Traffic lights for everyone: http://t.co/6ILqgjWc
— Matteo Niccoli (he/him) (@My_Carta) February 20, 2012
I really like the idea of making a traffic light that works for everyone: for people with full color vision and people with color vision deficiencies. In fact, I think we should do the same with our color palettes. Why do I say that?
Take a look at Figure 1 below. This is a map of the Bouguer Gravity (terrain corrected Bouguer Gravity to be precise) in Southern Tuscany, colored using a rainbow palette. I intentianally left out the colorbar. For a moment ignore the sharp gradient changes at the yellow and cyan color (that is one of the topics of my upcoming series “The rainbow is dead…long live the rainbow!”). Can you tell which color is representing high values an which low? If you have used a mnemonic like ROY B GIV and can tell that highs are towards the Southwest and lows towards the Northeast, then you are right and you also have full color vision, just like me. Great, because this post is exacly for us, the “normals”.
Figure 1
Take now a look at Figure 2:
Post by @stephenwestland about the place of indigo in the rainbow. Should it be there? #visualization #color #science http://t.co/CKPBi3ME
— Matteo Niccoli (he/him) (@My_Carta) November 14, 2011
Post by @stephenwestland on the origin of Newton's non-spectral purple hue: why is hue circular? #color #science #hue http://t.co/jgCK4ydB
— Matteo Niccoli (he/him) (@My_Carta) November 14, 2011
Literally!
This is a PA ulnar deviation x-ray of my left wrist from last month, which gives a good view of the scaphoid bone from above.
The bone is chipped in the area pointed by the arrow, due to a fall that occurred 20 or so years ago. Somewhere in there, there’s also a tiny detached fragment of cartilage that calcified (as seen in a CT scan at the time). I was lucky, because typically the result of a fall with outstretched hand for people aged 17-40 is the scaphoid fracture, which are known to have unpredictable healing. Lately, however, due to a tendonitis, the fragment too is acting out. I’m left handed so this is causing some trouble, and that’s why the recent x-rays.