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).
Last year, in a post titled Unweaving the rainbow, Matt Hall described our joint attempt to make a Python tool for recovering digital data from scientific images (and seismic sections in particular), without any prior knowledge of the colormap. Please check our GitHub repositoryfor the code and slides, andwatch Matt’s talk (very insightful and very entertaining) from the 2017 Calgary Geoconvention below:
One way to use the app is to get an image with unknown, possibly awful colormap, get the data, and re-plot it with a good one.
So it might come as a surprise to some, but this post is a lifesaver for those that really do like rainbow-like colormaps. I discuss a Python method to equalize colormaps so as to render them perceptual. The method is based in part on ideas from Peter Kovesi’s must-read paper – Good Colour Maps: How to Design Them – and the Matlab function equalisecolormap, and in part on ideas from some old experiments of mine, described here, and a Matlab prototype code (more details in the notebook for this post).
Let’s get started. Below is a time structure map for a horizon in the Penobscot 3D survey(offshore Nova Scotia, licensed CC-BY-SA by dGB Earth Sciences and The Government of Nova Scotia). Can you clearly identify the discontinuities in the southern portion of the map? No?
OK, let me help you. Below I am showing the map resulting from running a Sobel filter on the horizon.
This is much better, right? But the truth is that the discontinuities are right there in the original data; some, however, are very hard to see because of the colormap used (nipy spectral, one of the many Matplotlib cmaps), which introduces perceptual artifacts, most notably in the green-to-cyan portion.
In the figure below, in the first panel (from the top) I show a plot of the colormap’s Lightness value (obtained converting a 256-sample nipy spectral colormap from RGB to Lab) for each sample; the line is coloured by the original RGB colour. This erratic Lightness profile highlights the issue with this colormap: the curve gradient changes magnitude several times, indicating a nonuniform perceptual distance between samples.
In the second panel, I show a plot of the cumulative sample-to-sample Lightness contrast differences, again coloured by the original RGB colours in the colormap. This is the best plot to look at because flat spots in the cumulative curve correspond to perceptual flat spots in the map, which is where the discontinuities become hard to see. Notice how the green-to-cyan portion of this curve is virtually horizontal!
That’s it, it is simply a matter of very low, artificially induced perceptual contrast.
Solutions to this problem: the obvious one is to Other NOT use this type of colormaps (you can learn much about which are good perceptually, and which are not, in here); a possible alternative is to fix them. This can be done by re-sampling the cumulative curve so as to give it constant slope (or constant perceptual contrast). The irregularly spaced dots at the bottom (in the same second panel) show the re-sampling locations, which are much farther apart in the perceptually flat areas and much closer in the more dipping areas.
The third panel shows the resulting constant (and regularly sampled) cumulative Lightness contrast differences, and the forth and last the final Lightness profile which is now composed of segments with equal Lightness gradient (in absolute value).
Here is the structure map for the Penobscot horizon using the nipy spectum before and after equalization on top of each other, to facilitate comparison. I think this method works rather well, and it will allow continued use of their favourite rainbow and rainbow-like colormaps by hard core aficionados.
In a recent post titled Unweaving the rainbow, Matt Hall described our joint attempt (partly successful) to create a Python tool to enable recovery of digital data from any pseudo-colour scientific image (and a seismic section in particular, like the one in Figure 1), without any prior knowledge of the colormap.
Figure 1. Test image: a photo of a distorted seismic section on my wall.
Please check our GitHub repositoryfor the code and slides andwatch Matt’s talk (very insightful and very entertaining) from the 2017 Calgary Geoconvention below:
In the next two post, coming up shortly, I will describe in greater detail my contribution to the project, which focused on developing a computer vision pipeline to automatically detect where the seismic section is located in the image, rectify any distortions that might be present, and remove all sorts of annotations and trivia around and inside the section. The full workflow is included below (with sections I-VI developed to date):
I – Image preparation, enhancement:
Convert to gray scale
Optional: smooth or blur to remove high frequency noise
II – Find seismic section:
Convert to binary with adaptive or other threshold method
Find and retain only largest object in binary image
Fill its holes
Apply opening and dilation to remove minutiae (tick marks and labels)
III – Define rectification transformation
Detect contour of largest object find in (2). This should be the seismic section.
Approximate contour with polygon with enough tolerance to ensure it has 4 sides only
Sort polygon corners using angle from centroid
Define new rectangular image using length of largest long and largest short sides of initial contour
Estimate and output transformation to warp polygon to rectangle
IV – Warp using transformation
V – Blanking annotations inside seismic section (if rectangular):
Start with output of (4)
Pre-process and apply canny filter
Find contours in the canny filter smaller than input size
Sort contours (by shape and angular relationships or diagonal lengths)
Loop over contours:
If approximation has 4 points AND the 4 semi-diagonals are of same length: fill contour and add to mask
VI – Use mask to remove text inside rectangle in the input and blank (NaN) the whole rectangle.
VII – Optional: tools to remove arrows and circles/ellipses:
For arrows – contours from (4) find ones with 7 sizes and low convexity (concave) or alternatively Harris corner and count 7 corners, or template matching
For ellipses – template matching or regionprops
VIII – Optional FFT filters to remove timing lines and vertical lines
The first post focuses on the image pre-processing and enhancement, and the detection of the seismic line (sections I and II, in green); the second one deals with the rectification of the seismic (sections IV to V, in blue). They are not meant as full tutorials, rather as a pictorial road map to (partial) success, but key Python code snippets will be included and discussed.
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.
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.
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.
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).
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 , 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  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).
 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.
 The green chip is almost completely covered by the orange chip.
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.
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.
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.
Figure 2: logspiral colormap trajectory in CIELab a-b plane
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).
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.
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.
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.
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
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])';
lab1 = horzcat(L1int,lab(:,2),lab(:,3));
%% new rainbow
% convert back from Lab to RGB colour space
swtth = colorspace('RGB<-Lab',lab1);
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.