x lines of Python: Let's play golf!

Normally in the x lines of Python series, I'm trying to do something useful in as few lines of code as possible, but — and this is important — without sacrificing clarity. Code golf, on the other hand, tries solely to minimize the number of characters used, and to heck with clarity. This might, and probably will, result in rather obfuscated code.

So today in x lines, we set x = 1 and see what kind of geophysics we can express. Follow along in the accompanying notebook if you like.

A Ricker wavelet

One of the basic building blocks of signal processing and therefore geophysics, the Ricker wavelet is a compact, pulse-like signal, often employed as a source in simulation of seismic and ground-penetrating radar problems. Here's the equation for the Ricker wavelet:

$$ A = (1-2 \pi^2 f^2 t^2) e^{-\pi^2 f^2 t^2} $$

where \(A\) is the amplitude at time \(t\), and \(f\) is the centre frequency of the wavelet. Here's one way to translate this into Python, more or less as expressed on SubSurfWiki:

import numpy as np 
def ricker(length, dt, f):
    """Ricker wavelet at frequency f Hz, length and dt in seconds.
    """
    t = np.arange(-length/2, length/2, dt)
    y = (1.0 - 2.0*(np.pi**2)*(f**2)*(t**2)) * np.exp(-(np.pi**2)*(f**2)*(t**2))
    return t, y

That is alredy pretty terse at 261 characters, but there are lots of obvious ways, and some non-obvious ways, to reduce it. We can get rid of the docstring (the long comment explaining what the function does) for a start. And use the shortest possible variable names. Then we can exploit the redundancy in the repeated appearance of \(\pi^2f^2t^2\)... eventually, we get to:

def r(l,d,f):import numpy as n;t=n.arange(-l/2,l/2,d);k=(n.pi*f*t)**2;return t,(1-2*k)/n.exp(k)

This weighs in at just 95 characters. Not a bad reduction from 261, and it's even not too hard to read. In the notebook accompanying this post, I check its output against the version in our geophysics package bruges, and it's legit:

The 95-character Ricker wavelet in green, with the points computed by the function in BRuges.

The 95-character Ricker wavelet in green, with the points computed by the function in BRuges.

What else can we do?

In the notebook for this post, I run through some more algorithms for which I have unit-tested examples in bruges:

To give you some idea of why we don't normally code like this, here's what the Aki–Richards solution looks like:

def r(a,c,e,b,d,f,t):import numpy as n;w=f-e;x=f+e;y=d+c;p=n.pi*t/180;s=n.sin(p);return w/x-(y/a)**2*w/x*s**2+(b-a)/(b+a)/n.cos((p+n.arcsin(b/a*s))/2)**2-(y/a)**2*(2*(d-c)/y)*s**2

A bit hard to debug! But there is still some point to all this — I've found I've had to really understand Python's order of mathematical operations, and find different ways of doing familiar things. Playing code golf also makes you think differently about repetition and redundancy. All good food for developing the programming brain.

Do have a play with the notebook, which you can even run in Microsoft Azure, right in your browser! Give it a try. (You'll need an account to do this. Create one for free.)


Many thanks to Jesper Dramsch and Ari Hartikainen for helping get my head into the right frame of mind for this silliness!

PRESS START

The dust has settled from the Subsurface Hackathon 2016 in Vienna, which coincided with EAGE's 78th Conference and Exhibition (some highlights). This post builds on last week's quick summary with more detailed descriptions of the teams and what they worked on. If you want to contact any of the teams, you should be able to track them down via the links to Twitter and/or GitHub.

A word before I launch into the projects. None of the participants had built a game before. Many were relatively new to programming — completely new in one or two cases. Most of the teams were made up of people who had never worked together on a project before; indeed, several team mates had never met before. So get ready to be impressed, maybe even amazed, at what members of our professional community can do in 2 days with only mild provocation and a few snacks.

Traptris

An 8-bit-style video game, complete with music, combining Tetris with basin modeling.

Team: Chris Hamer, Emma Blott, Natt Turner (all MSc students at the University of Leeds), Jesper Dramsch (PhD student, Technical University of Denmark, Copenhagen). GitHub repo.

Tech: Python, with PyGame.

Details: The game is just like Tetris, except that the blocks have lithologies: source, reservoir, and seal. As you complete a row, it disappears, as usual. But in this game, the row reappears on a geological cross-section beside the main game. By completing further rows with just-right combinations of lithologies, you build an earth model. When it's deep enough, and if you've placed sources rocks in the model, the kitchen starts to produce hydrocarbons. These migrate if they can, and are eventually trapped — if you've managed to build a trap, that is. The team impressed the judges with their solid gamplay and boisterous team spirit. Just installing PyGame and building some working code was an impressive feat for the least experienced team of the hackathon.

Prize: We rewarded this rambunctious team for their creative idea, which it's hard to imagine any other set of human beings coming up with. They won Samsung Gear VR headsets, so I'm looking forward to the AR version of the game.

Flappy Trace

A ridiculously addictive seismic interpretation game. "So seismic, much geology".

Team: Håvard Bjerke (Roxar, Oslo), Dario Bendeck (MSc student, Leeds), and Lukas Mosser (PhD student, Imperial College London).

Tech: Python, with PyGame. GitHub repo.

Details: You start with a trace on the left of the screen. More traces arrive, slowly at first, from the right. The controls move the approaching trace up and down, and the pick point is set as it moves across the current trace and off the screen. Gradually, an interpretation is built up. It's like trying to fly along a seismic horizon, one trace at a time. The catch is that the better you get, the faster it goes. All the while, encouragements and admonishments flash up, with images of the doge meme. Just watching someone else play is weirdly mesmerizing.

Prize: The judges wanted to recognize this team for creating such a dynamic, addictive game with real personality. They won DIY Gamer kits and an awesome book on programming Minecraft with Python.

Guess What!

Human seismic inversion. The player must guess the geology that produces a given trace.

Team: Henrique Bueno dos Santos, Carlos Andre (both UNICAMP, Sao Paolo), and Steve Purves (Euclidity, Spain)

Tech: Python web application, on Flask. It even used Agile's nascent geo-plotting library, g3.js, which I am pretty excited about. GitHub repo. You can even play the game online!

Details: This project was on a list of ideas we crowdsourced from the Software Underground Slack, and I really hoped someone would give it a try. The team consisted of a postdoc, a PhD student, and a professional developer, so it's no surprise that they managed a nice implementation. The player is presented with a synthetic seismic trace and must place reflection coefficients that will, she hopes, forward model to match the trace. She may see how she's progressing only a limited number of times before submitting her final answer, which receives a score. There are so many ways to control the game play here, I think there's a lot of scope for this one.

Prize: This team impressed everyone with the far-reaching implications of the game — and the rich possibilities for the future. They were rewarded with SparkFun Digital Sandboxes and a copy of The Thrilling Adventures of Lovelace and Babbage.

DiamondChaser

aka DiamonChaser (sic). A time- and budget-constrained drilling simulator aimed at younger players.

Team: Paul Gabriel, Björn Wieczoreck, Daniel Buse, Georg Semmler, and Jan Gietzel (all at GiGa infosystems, Freiberg)

Tech: TypeScript, which compiles to JS. BitBucket repo. You can play the game online too!

Details: This tight-knit group of colleagues — all professional developers, but using unfamiliar technology — produced an incredibly polished app for the demo. The player is presented with a blank cross section, and some money. After choosing what kind of drill bit to start with, the drilling begins and the subsurface is gradually revealed. The game is then a race against the clock and the ever-diminishing funds, as diamonds and other bonuses are picked up along the way. The team used geological models from various German geological surveys for the subsurface, adding a bit of realism.

Prize: Everyone was impressed with the careful design and polish of the app this team created, and the quiet industry they brought to the event. They each won a CellAssist OBD2 device and a copy of Charles Petzold's Code.

Some of the participants waiting for the judges to finish their deliberations. Standing, from left: Håvard Bjerke, Henrique Bueno dos Santos, Steve Purves. Seated: Jesper Dramsch, Lukas Mosser, Natt Turner, Emma Blott, Dario Bendeck, Carlos André, Björn Wieczoreck, Paul Gabriel.

Some of the participants waiting for the judges to finish their deliberations. Standing, from left: Håvard Bjerke, Henrique Bueno dos Santos, Steve Purves. Seated: Jesper Dramsch, Lukas Mosser, Natt Turner, Emma Blott, Dario Bendeck, Carlos André, Björn Wieczoreck, Paul Gabriel.

Credits and acknowledgments

Thank you to all the hackers for stepping into the unknown and coming along to the event. I think it was everyone's first hackathon. It was an honour to meet everyone. Special thanks to Jesper Dramsch for all the help on the organizational side, and to Dragan Brankovic for taking care of the photography.

The Impact HUB Vienna was a terrific venue, providing us with multiple event spaces and plenty of room to spread out. HUB hosts Steliana and Laschandre were a great help. Der Mann produced the breakfasts. Il Mare pizzeria provided lunch on Saturday, and Maschu Maschu on Sunday.

Thank you to Kristofer Tingdahl, CEO of dGB Earth Sciences and a highly technical, as well as thoughtful, geoscientist. He graciously agreed to act as a judge for the demos, and I think he was most impressed with the quality of the teams' projects.

Last but far from least, a huge Thank You to the sponsor of the event, EMC, the cloud computing firm that was acquired by Dell late last year. David Holmes, the company's CTO (Energy) was also a judge, making an amazing opportunity for the hackers to show off their skills, and sense of humour, to a progressive company with big plans for our industry.

Minecraft for geoscience

The Isle of Wight , complete with geology. ©Crown copyright. 

The Isle of Wight, complete with geology. ©Crown copyright. 

You might have heard of Minecraft. If you live with any children, then you definitely have. It's a computer game, but it's a little unusual — there isn't really a score, and the gameplay has no particular goal or narrative, leaving everything to the player or players. It's more like playing with Lego than, say, playing chess or tennis or paintball. The game was created by Swede Markus Persson and then marketed by his company Mojang. Microsoft bought Mojang in September last year for $2.5 billion. 

What does this have to do with geoscience?

Apart from being played by 100 million people, the game has attracted a lot of attention from geospatial nerds over the last 12–18 months. Or rather, the Minecraft environment has. The game chiefly consists of fabricating, placing and breaking 1-m-cubed blocks of various materials. Even in normal use, people create remarkable structures, and I don't just mean 'big' or 'cool', I mean truly remarkable. So the attention from the British Geological Survey and the Danish Geodata Agency. If you've spent any time building geocellular models, then the process of constructing elaborate digital models is familiar to you. And perhaps it's not too big a leap to see how the virtual world of Minecraft could be an interesting way to model the subsurface. 

Still I was surprised when, chatting to Thomas Rapstine at the Geophysics Hackathon in Denver, he mentioned Joe Capriotti and Yaoguo Li, fellow researchers at Colorado School of Mines. Faced with the problem of building 3D earth models for simulating geophysical experiments — a problem we've faced with modelr.io — they hit on the idea of adapting Minecraft models. This is not just a gimmick, because Minecraft is specifically designed for simulating and manipulating landscapes.

The Minecraft model (left) and synthetic gravity data (right). Image ©2014 SEG and Capriotti & Li. Used in acordance with SEG's  permissions . 

The Minecraft model (left) and synthetic gravity data (right). Image ©2014 SEG and Capriotti & Li. Used in acordance with SEG's permissions

If you'd like to dabble in geospatial Minecraft yourself, the FME software from Safe now has a standardized way to get Minecraft data into and out of the environment. Essentially they treat the blocks as point clouds (e.g. as you might get from Lidar or a laser scan), so they can do conventional operations, such as differences or filtering, with the software. They recorded a webinar on the subject yesterday.

Minecraft is here to stay

There are two other important angles to Minecraft, both good reasons why it will probably be around for a while, and probably both something to do with why Microsoft bought Mojang...

  1. It is a programming gateway drug. Like web coding, and image processing, Minecraft might be another way to get people, especially young people, interested in computing. The tiny Linux machine Raspberry Pi comes with a version of the game with a full Python API, so you can control the game programmatically.  
  2. Its potential beyond programming as a STEM teaching aid and engagement tool. Here's another example. Indeed, the United Nations is involved in Block By Block, an effort around collaborative public space design echoing the Blockholm project, an early attempt to explore social city planning in the tool.

All of which is enough to make me more curious about the crazy-sounding world my kids have built, with its Houston-like city planning: house, school, house, Home Sense, house, rocket launch pad...

References

Capriotti, J and Yaoguo Li (2014) Gravity and gravity gradient data: Understanding their information content through joint inversions. SEG Technical Program Expanded Abstracts 2014: pp. 1329-1333. DOI 10.1190/segam2014-1581.1 

The thumbnail image is from an image by Terry Madeley.

UPDATE: Thank you to Andy for pointing out that Yaoguo Li is a prof, not a student.