Tag Archives: colormap

Upcoming book: 52 things you should know about Geocomputing

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I am very excited to write that, after a successful second attempt at collecting enough essays, the book 52 Things You Should Know About Geocomputing, by Agile Libre, is very likely to become a reality.

*** July 2020 UPDATE ***

This project got a much needed boost during the hackathon at the 2020 Transform virtual event. Watch the video recording on the group YouTube channel here.

*********************

In one of the three chapter I submitted for this book, Prototype colourmaps for fault interpretation, I talk about building a widget for interactive generation of grayscale colourmaps with sigmoid lightness. The whole process is well described in the chapter and showcased in the accompanying GitHub repo.

This post is an opportunity for me to reflect on how revisiting old projects is very important. Indeed, I consider it an essential part of how I approach scientific computing, and a practical way to incorporate new insights, and changes (hopefully betterments) in your coding abilities.

In the fist version of the Jupyter notebook, submitted in 2017, all the calculations and all the plotting commands where packed inside a single monster function that was passed to ipywidgets.interact. Quite frankly, as time passed this approach seemed less and less Phytonic (aka mature) and no longer representative of my programming skills and style, and increased understanding of widget objects.

After a significant hiatus (2 years) I restructured the whole project in several ways:
– Converted Python 2 code to Python 3
– Created separate helper functions for each calculation and moved them to the top to improve on both clarity and reusability of the code.
– Improved and standardized function docstrings
– Optimized and reduced the number of parameters
– Switched from interact to interactive to enable access to the colormaparray in later cells (for printing, further plotting, and exporting).

The new notebook is here.

In a different chapter in the book I talk at more length about the need to Keep on improving your geocomputing projects.

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Reinventing the color wheel – part 2

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In the first post of this series I argued that we should not build colormaps for azimuth (or phase) data by interpolating linearly between fully saturated hues in RGB or HSL space.

A first step towards the ideal colormap for azimuth data would be to interpolate between isoluminant colours instead. Kindlmann et al. (2002) published isoluminant RGB values for red, yellow, green, cyan, blue, and magenta based on a user study. The code in the next block show how to interpolate between those published colours to get 256-sample R, G, and B arrays (with magenta repeated at both ends), which can then be combined into a isoluminant colormap for azimuth data.

01 r = np.array([0.718, 0.847, 0.527, 0.000, 0.000, 0.316, 0.718])
02 g = np.array([0.000, 0.057, 0.527, 0.592, 0.559, 0.316, 0.000])
03 b = np.array([0.718, 0.057, 0.000, 0.000, 0.559, 0.991, 0.718])
04 x = np.linspace(0,256,7)
05 xnew = np.arange(256)
06 r256 = np.interp(xnew, x, r)
07 g256 = np.interp(xnew, x, g)
08 b256 = np.interp(xnew, x, b)

This is a good example in general of how to interpolate to a finer sampling one or more sequence of values using the interp function from the Numpy library. In line 04 we define 7 evenly spaced points between 0 and 255; this will be the sample coordinate for the r, g, and b colours created in lines 01-03. In line 05 we create the new coordinates we will be interpolating r, g, and b values at in lines 06-08 (all integers between 0 and 256). The full code will come in the Notebook accompanying the last post in this series.

This new colormap is used in the bottom map of the figure below, whereas in the top map we used a conventional HSV azimuth colormap (both maps show the dip azimuth calculated on the Penobscot horizon). The differences are subtle, but with the isoluminant colormap we are guaranteed there are no perceptual artifacts due to the random variations in lightness of the fully saturated HSV colors.

Azimuth_compare

Another possible strategy to create a perceptual colormap for azimuth data would be to set lightness and chroma to constant values in LCH space and interpolate between hues. This is the Matlab colormap I previously created, and shown in Figure 4 of New Matlab isoluminant colormap for azimuth data. In the next post, I will show how to do this in Python.

Read more on colors and seismic data

The last two posts on Agile show you how to corender seismic amplitude and continuity from a time slice using a 2D colormap,  and then how to corender 3 attributes from a horizon slice.

Reference

Kindlmann, E. et al. (2002). Face-based Luminance Matching for Perceptual Colour map Generation – Proceedings of the IEEE conference on Visualization.

Reinventing the color wheel – part 1

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In New Matlab isoluminant colormap for azimuth data I showcased a Matlab colormap that I believe is perceptually superior to the conventional, HSV-based colormaps for azimuth data, in that it does not superimposes on the data the color artifacts that plague all rainbows. However, it still has a limitation, which is that the main colours do not correspond exactly to the four compass directions N, E, W, and S.

My intention with this series is to go back to square one, deconstruct the conventional colormaps for azimuth, and build a new one that has all the desired properties of both perceptual linearity, and correct location of the main colors. All reproducible in Python.

If we wanted to build from scratch a colormap for azimuth (or phase) data the main tasks would be to generate a sequence of distinguishable colours at opposite quadrants, or compass directions (like 0 and 180 degrees, or N and S), and to wrap around the sequence with the same colour at the two ends.

But to do that, we should avoid interpolating linearly between fully saturated hues in RGB or HSL space.

To illustrate why, it is useful to look at the figure below. On the left is a hue circle with primary, secondary, and tertiary colours in a counter-clockwise sequence: red, rose, magenta, violet, blue, azure, cyan, aquamarine, electric green, chartreuse, yellow, and orange. The colour chips are placed at evenly spaced angular distances according to their hue (in radians).

hue-wheel-compare

Left, primary, secondary, and tertiary colour chips arranged using hue for angular distance; right, the same colour chips arranged using intensity for angular distance.

This looks familiar and seems like a natural ordering of colors, so we may be tempted in building a colormap, to just take that sequence, wrap it around at the red (or the magenta) and linearly interpolate to 256 colours to get a continuous colormap [1], and use it for azimuth data, which is how usually the conventional azimuth colormaps are built.

On the right side in the figure the chips have been rearranged according to their intensity on a counter-clockwise sequence from 0 to 255 with 0 at three hours; so, for example blue, which is the darkest colour with an intensity of 29, is close to the beginning of the sequence, and yellow, the brightest with an intensity of 225, is close to the end. Notice that the chips are no longer equidistant.

The most striking is that the blue and the yellow chips are more separated than the other chips, and for this reason blue and yellow features seem to stand out a lot more in a map when using this color sequence, which can be both distracting and confusing. A good example is Figure 3 in New Matlab isoluminant colormap for azimuth data.

Also, yellow and red, being two chips apart in the left circle in the figure above, are used to colour azimuths 60 degrees apart, and so do cyan and green. However, if we look at the right circle, we realize that the yellow and red chips are much further apart than the cyan and green chips [2] in the perceptual dimension of intensity; therefore, features colored in yellow and red  could be perceived as much further apart (in azimuth) than cyan and green.

These differences may be subtle, but in my opinion they become important when dip azimuth is combined with other attributes, perhaps using a 3D colormap, and the resulting map is used for detailed structural interpretation. There is a really good example of this type of 3D colormap in Chopra and Marfurt (2007), where dip azimuth is rendered with hue modulation, dip magnitude with saturation modulation, and coherence with lightness modulation.

A code snippet with the main Python commands to generate the two polar scatterplots in the figure is listed, and explained below. The full code can be found in this Jupiter Notebook.

01 import matplotlib.colors as clr
02 keys=['red', '#FF007F', 'magenta', '#7F00FF', 'blue', '#0080FF','cyan', '#00FF80',
'#00FF00', '#7FFF00', 'yellow', '#FF7F00']
03 my_cmap = clr.ListedColormap(keys)
04 x = np.arange(12)
05 color = my_cmap(x)
06 n = 12
07 theta = 2*np.pi*(np.linspace(0,1,13)) 
08 r = np.ones(13)*2.5
09 area = 200*r**2 # size of color chips
10 c = plt.scatter(theta, r, c=color, s=area)
11 theta_i = 2*np.pi*(sorted_intensity/255.0)
12 colors = my_sorted_cmap(np.arange(12))
13 c = plt.scatter(theta_i, r, c=colors, s=area)

In line 01 we import the Colors module from the Matplotlib library, then line 02 creates the desired sequence of colours (red, rose, magenta, violet, blue, azure, cyan, aquamarine, electric green, chartreuse, yellow, and orange) using either the name or Hex code, and line 03 generates the colormap. Then we use lines 04 and 05 to assign colours to the chips in the first scatterplot (left), and lines 06, 07, and 09 to specify the number of chips, the angular distances between chips, and the area of the chips, respectively. Line 10 generates the plot. The modifications in lines 11-14 will result in the scatterplot on the right side in the figure (the sorted intensity is calculated in much the same way as in my Geophysical tutorial – How to evaluate and compare colormaps in Python).

 

[1] Or, perhaps, just create 12 discrete colour classes to group azimuth values in bins of pi/6 (30 degrees) each, and wrap around again at the magenta, to generate a discrete colormap.

[2] The green chip is almost completely covered by the orange chip.

Logarithmic spiral, nautilus, and rainbow

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The other day I stumbled into an interesting article on The Guardian online: The medieval bishop who helped to unweave the rainbow. In the article I learned for the first time of Robert Grosseteste, a 13th century British scholar (with an interesting Italian last name: Grosse teste = big heads) who was also the Bishop of Lincoln.

The Bishops’ interests and investigations covered diverse topics, making him a pre-renaissance polymath; however, it is his 1225 treatise on colour, the De Colore, that is receiving much attention.

In a recent commentary on Nature Physics (All the colours of the rainbow), and reference therein (A three-dimensional color space from the 13th century),  Smithson et al. (who also recently published a new critical edition/translation of the treatise with analysis and critical commentaries) analyze the 3D colorspace devised by Grosseteste, who claimed it allows the generation of all possible colours and to describe the variations of colours among different rainbows.

As we learn from Smithson et al., Grosseteste’s colorpsace had three dimensions, quantified by physical properties of the incident light and the medium: these are the scattering angle (which produces variation of hue within a rainbow), the purity of the scattering medium (which produces variation between different rainbows and is linked to the size of the water droplets in the rainbow), and the altitude of the sun (which produces variation in the light incident on a rainbow). The authors were able to model this colorspace and also to show that the locus of rainbow colours generated in that colorspace forms a spiral surface (a family of spiral curves, each form a specific rainbow) in  the perceptual CIELab colorspace.

I found this not only fascinating – a three-dimensional, perceptual colorspace from the 13th century!! – but also a source of renewed interest in creating the perfect perceptual colormaps by spiralling through CIELab.

My first attempt of colormap spiralling in CIELab, CubicYF, came to life by selecting hand-picked colours on CIELab colour charts at fixed lightness values (found in this document by Gernot Hoffmann). The process was described in this post, and you can see an animation of the spiral curve in CIELab space (created with the 3D color inspector plugin in ImageJ) in the video below:

Some time later, after reading this post by Rob Simmon (in particular the section on the NASA Ames Color Tool), and after an email exchange with Rob, I started tinkering with the idea of creating perceptual rainbow colormaps in CIELab programmatically, by using a helix curve or an Archimedean spiral, but reading Smithson et al. got me to try the logarithmic spiral.

So I started my experiments with a warm-up and tried to replicate a Nautilus using a logarithmic spiral with a growth ratio equal to 0.1759. You may have read that the rate at which a Nautilus shell grows can be described by the golden ratio phi, but in fact the golden spiral constructed from a golden rectangle is not a Nautilus Spiral (as an aside, as I was playing with the code I recalled reading some time ago Golden spiral, a nice blog post (with lots of code) by Cleve Moler, creator of the first version of Matlab,  who simulated a golden spiral using a continuously expanding sequence of golden rectangles and inscribed quarter circles).

My nautilus-like spiral, plotted in Figure 1, has a growth ratio of 0.1759 instead of the golden ratio of 1.618.

nautilus logarithmic spiral with growth ratio = 0.1759

Figure 1: nautilus-like spiral with growth ratio = 0.1759

And here’s the colormap (I called it logspiral) I came up with after a couple of hours of hacking: as hue cycles from 360 to 90 degrees, chroma spirals outwardly (I used a logarithmic spiral with polar equation c1*exp(c2*h) with a growth ratio c2 of 0.3 and a constant c1 of 20), and lightness increases linearly from 30 to 90.

Figure 2 shows the trajectory in the 2D CIELab a-b plane; the colours shown are the final RGB colours. In Figure 3 the trajectory is shown in 3D CIELab space. The coloured lightness profiles were made using the Colormapline submission from the Matlab File Exchange.

2D logspiral colormap in CIELab a-b plane

Figure 2: logspiral colormap trajectory in CIELab a-b plane

logspiral colormap trajectory in CIELab 3D space

Figure 3: logspiral colormap in CIELab 3D space

 

N.B. In creating logspiral, I was inspired by Figure 2 in the Nature Physics paper, but there are important differences in terms of colorspace, lightness profile and perception: I am not certain their polar coordinates are equivalent to Lightness, Chroma, and Hue, although they could; and, more importantly, the three-dimensional spirals based on Grosseteste’s colorpsace go from low lightness at low scattering angles to much higher values at mid scattering angles, and then drop again at high scattering angle (remember that these spirals describe real world rainbows), whereas lightness in logspiral lightness is strictly monotonically increasing.

In my next post I will share the Matlab code to generate a full set of logspiral colormaps sweeping the hue circle from different staring colours (and end colors) and also the slower-growing logarithmic spirals to make a set of monochromatic colormaps (similar to those in Figure 2 in the Nature Physics paper).

 

Convert Matlab colormap to Surfer colormap

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In the comment section of my last post, Steve asked if I had code to generate a Surfer.clr file from my Matlab colormaps.

Some time ago I did write a simple Matlab .m file to write a colormap to a variable with the correct Surfer format, but at the time I was content to have the variable output to a .txt file, which I would then open in a text editor to add a 1-line header and change the file extension to .clr.

I went back, cleaned up the script, and automated all the formatting. This is my revised code (you may need to change the target directory c:\My Documents\MATLAB):

%% Make a Matlab colormap
% one of the colormaps from my function, Perceptually improved colormaps
sawtooth=pmkmp(256,'swtth');

%% Initialize variable for Surfer colormap
%reduce to 101 samples
sawtooth_surfer=zeros(101,5);
%% Make Surfer colormap
% add R,G,B columnns
for i=1:3 
sawtooth_surfer(:,i+1)=round(interp1([1:1:256]',sawtooth(:,i),(linspace(1,256,101))')*255);
end
% add counter and alpha (opacity) columns
sawtooth_surfer(:,1)=linspace(0,100,101);
sawtooth_surfer(:,5)=ones(101,1)*255;
%% Create output file 
filename='c:\My Documents\MATLAB\stth4surf.clr'; 
fileID=fopen(filename,'wt');
%%  Write Surfer colormap header
fprintf(fileID,'ColorMap 2 1\n');
fclose(fileID);
 
%% Add the colormap:
dlmwrite('c:\My Documents\MATLAB\stth4surf.clr',...
    sawtooth_surfer,'precision',5,'delimiter','\t', '-append');

Spectral lightness rainbow colormap

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Spectral lightness rainbow

Quick post to share my replica of Ethan Montag ‘s Spectral lightness colormap from this paper. My version has a linear Lightness profile (Figure 1) that increases monotonically from 0 (black) to 100 (white) while Hue cycles from 180 to 360 degrees and then wraps around and continues from 0 to 270.

You can download the colormap files (comma separated in MS Word .doc format) with RGB values in 0-1 range and 0-255 range.

L-plot

Figure 1

Spectral-L

Figure 2

Matlab code

To run this code you will need Colorspace, a free function from Matlab File Exchange, for the color space transformations.

%% generate Chroma, Lightness, Hue components
h2=linspace(0,270,60*2.56);
h1=linspace(180,360,103);
h=horzcat(h1,h2);
c=ones(1,256)*25;
l=linspace(0,100,256);
%% merge together
lch = vertcat(l,c,h)';
%% convert to RGB
rgb = colorspace('LCH->rgb',lch);
%% Plot color-coded lightness profile
figure;
h=colormapline(1:1:256,lch(:,1),[],rgb);
set(h,'linewidth',2.8);
title('Montag Spectral L* lightness plot ','Color','k','FontSize',12,'FontWeight','demi');
%%  Pyramid test data
PY=zeros(241,241);
for i = 1:241
    temp=(0:1:i-1);
      PY(i,1:i)=temp(:);
end
test=PY.';
test=test-1;
test(test==-1)=0;
test1=test([2:1:end,1],:);
PY1=PY+test1;
PY2=fliplr(PY1);
PY3= flipud(PY1);
PY4=fliplr(PY3);
GIZA=[PY1,PY2;PY3,PY4].*2;
x=linspace(1,756,size(GIZA,1));
y=x;
[X,Y]=meshgrid(x,y);
clear i test test1 PY PY1 PY2 PY3 PY4 temp;

%% display Pyramid surface
fig1=figure;
surf(X,Y,GIZA,GIZA,'FaceColor','interp','EdgeColor','none');
view(-35,70);
colormap(rgb);
axis off;
grid off;
colorbar;
% set(fig1,'Position',[720 400 950 708]);
% set(fig1,'OuterPosition',[716 396 958 790]);
title('Montag Spectral L*','Color','k','FontSize',12,'FontWeight','demi');

Aknowledgements

The coloured lightness profiles were made using the Colormapline submission from the Matlab File Exchange.

New rainbow colormap: sawthoot-shaped lightness profile

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Why another rainbow

In the comment section of my last post Steve Eddins from Mathworks reported that some Matlab users prefer Jet to Parula, the new default perceptual colormap in Matlab, because within certain ranges Jet affords a greater contrast, intended as the rate of change in lightness.

My counter-argument to that is that yes, some data may benefit from being displayed using Jet (in terms of contrast, and hence the power to resolve smaller anomalies) because of those areas of very steep rate of change of lightness, like the blue to cyan and yellow to red portions (see Figure 1). But the price one has to pay is that there is an area of very low gradient (a greenish band between cyan and yellow) where there’s nearly no contrast, which would obfuscate subtle anomalies in the data. On top of that there’s no control of where each of those areas are located, so a lot of effort has to go into trying to fit those regions of artificially high contrast to the portion of data of interest.

L_profile_jet_cl

Figure 1

Because of their high lightness, the yellow and cyan artificial edges also cause problems. In his latest blog post Steve uses a test pattern do demonstrate how they make the interpretation of trivial structures more difficult. He also explains why they occurr in some locations and not others in the first place. I wonder if the resulting regions of high lightness juxtaposed to regions of low lightness could be chromatic Mach bands.

Additionally, as Steve points out, the low-contrast juxtaposition of dark red and dark blue bands creates the visual illusion of depth (Chromostereopsis) in other positions of the test pattern, creating further confusion.

But I have some good news for the hardcore fans of Jet, and rainbow colormaps in general. I created a rainbow with a sawtooth-shaped lightness profile made up of 5 ramps, each with the same  rate of change in lightness and total lightness change of 60, and alternatively negative and positive signs. This is shown in Figure 2, and replaces the lightness profile of a basic 6-color rainbow (magenta-blue-cyan-green-yellow-red) shown in Figure 3.

Figure 2

Figure 2

Figure 2

Figure 3

With this rainbow users have the ability to apply greater contrast to their data to boost small anomalies, but in a more controlled way. The colormap is available with my File Exchange function, Perceptually improved colormaps. Below is the Matlab code I used to generate the new rainbow.

Matlab code

To run this code you will need Colorspace, a free function from Matlab File Exchange, for the color space transformations.

%% basic 6-colour rainbow
% create RGB components
m = [1, 0, 1]; % magenta
b = [0, 0, 1]; % blue
c = [0, 1, 1]; % cyan
g = [0, 1, 0]; % green
y = [1, 1, 0]; % yellow
r = [1, 0, 0]; % red
% concatenate components
rgb = vertcat(m,b,c,g,y,r);
% interpolate to 256 colours
rainbow=interp1(linspace(1, 256, 6),rgb,[1:1:256]);
%% calculate Lab components
% convert from RGB to Lab colour space
% requires this function: Colorspace transforamtions
% www.mathworks.com/matlabcentral/fileexchange/28790-colorspace-transformations
lab = colorspace('RGB->Lab',rainbow);

%% replace random lightness profile with sawtooth-shaped profile
% contrast (magnitude of lightness change) between
% each pair of adjeacent colors set to 60
L1 = [90, 30, 90, 30, 90, 30];
% interpolate to 256 lightness values
L1int = interp1(linspace(1, 256, 6),L1,[1:1:256])';
% replace
lab1 = horzcat(L1int,lab(:,2),lab(:,3));
%% new rainbow
% convert back from Lab to RGB colour space
swtth = colorspace('RGB<-Lab',lab1);

Test results

Figures 4, 5, and 6 show the three colormaps used with my Pyramid test surface (notice in Figure 5 that the green band artifact with this rainbow is even more pronounced than with jet). I welcome feedback.

Figure 4

Figure 4

Pyramid_basic_rainbow

Figure 5

Figure 4

Figure 6

Aknowledgements

The coloured lightness profiles were made using the Colormapline submission from the Matlab File Exchange.

 

Visualizing colormap artifacts

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In Evaluate and compare colormaps, I have shown how to extract and display the lightness profile of a colormap using Python. I do this routinely with colormaps, but I realize it takes an effort, and not all users may feel comfortable using code to test whether a colormap is perceptual or not.

This got me thinking that there is perhaps a need for a user-friendly, interactive tool to help identify colormap artifacts, and wondering how it would look like.

In a previous post, Comparing color palettes, I plotted the elevation for the South American continent from the Global Land One-km Base Elevation Project using four different color palettes. In Figure 1 below I plot again 3 of those: rainbow, linear lightness rainbow, and grayscale, respectively, from left to right. In maps like these some artifacts are very evident. For example there’s a classic film negative effect in the map on the left, where the Guiana Highlands and the Brazilian Highlands, both in blue, seem to stand lower than the Amazon basin, in violet. This is due to the much lower lightness (or alternatively intensity) of the colour blue compared to the violet.

South_America_maps_post

Figure 1

 

However, other artifacts are more subtle, like the inversion of the highest peaks in the Andes, which are coloured in red, relative to their surroundings, in particular the Altipiano, an endorheic basin that includes Lake Titicaca.

My idea for this tool is simple, and consists of two windows. The first is a basemap window which can display either a demo dataset or user data loaded from an ASCII grid file. In this window the user would interactively select a profile by building a polyline with point-and-click, like the one in Figure 2 in white.

South_America_map_window

Figure 2

The second window would show the elevation profile with the colour fill assigned based on the colormap, like in Figure 3 at the bottom (with colormap to the right), and with a profile of the corresponding colour intensities (on a scale 1-255) at the top.

In this view it is immediately evident that, for example, the two highest peaks near the center, coloured in red, are relative intensity lows. Another anomaly is the absolute intensity low on the right side, corresponding to the colour blue, where the elevation profile varies smoothly.

Figure 3

Figure 3

I created this concept prototype using a combination of Matlab, Python, and Surfer. I welcome suggestions for possible additional features, and would like to hear form folks interested in collaboration on a web app (ideally in Python).