Strategies for a revolution

This must be a record. It has taken me several months to get around to recording the talk I gave last year at EAGE in Vienna — Strategies for a revolution. Rather a gradiose title, sorry about that, especially over-the-top given that I was preaching to the converted: the workshop on open source. I did, at least, blog aobut the goings on in the workshop itself at the time. I even followed it up with a slightly cheeky analysis of the discussion at the event. But I never posted my own talk, so here it is:

Too long didn't watch? No worries, my main points were:

  1. It's not just about open source code. We must write open access content, put our data online, and push the whole culture towards openness and reproducibility. 
  2. We, as researchers, professionals, and authors, need to take responsibility for being more open in our practices. It has to come from within the community.
  3. Our conferences need more tutorials, bootcamps, , hackathons and sprints. These events build skills and networks much faster than (just) lectures and courses.
  4. We need something like an Open Geoscience Foundation to help streamline funding channels for open source projects and community events.

If you depend on open source software, or care about seeing more of it in our field, I'd love to hear your thoughts about how we might achieve the goal of having greater (scientific, professional, societal) impact with technology. Please leave a comment.

 

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.

Automated interpretation highlights

As you probably know by know, I've been at the EAGE conference in Vienna this week. I skipped out yesterday and flew over to the UK for a few days. I have already written plenty about the open source workshop, and I will write more soon about the hackathon. But I thought I'd pass on my highlights from the the Automated Interpretation session on Tuesday. In light of Monday's discussion, I made a little bit of a nuisance of myself by asking the same post-paper question every time I got the chance:

Can I use your code, either commercially or for free?

I'll tell you what the authors responded.


The universal character of salt

I especially enjoyed the presentation by Anders Waldeland and Anne Solberg (University of Oslo) on automatically detecting salt in 3D seismic. (We've reported on Anne Solberg's work before.) Anders described training eight different classifiers, from a simple nearest mean to a neural network, a supprt vector model, and a mixture of Gaussians classifier. Interestingly, but not surprisingly, the simplest model turned out to be the most effective at discrimination. He also tried a great many seismic attributes, letting the model choose the best ones. Three attributes consistently proved most useful: coherency, Haralick energy (a GLCM-based texture attribute), and the variance of the kurtosis of the amplitude distribution (how's that for meta?). What was especially interesting about his approach was that he was training the models on one dataset, and predicting on an entirely different 3D. The idea is that this might reveal the universal seismic characteristics of salt. When I asked the golden question, he said "Come and talk to me", which isn't a "yes", but it isn't a "no" either.

Waldeland and Solberg 2016. Salt probability in a North Sea dataset (left) and the fully tracked volume (right). The prediction model was trained on a Gulf of Mexico dataset. Copyright of the authors and EAGE, and used under a Fair Use claim.

Waldeland and Solberg 2016. Salt probability in a North Sea dataset (left) and the fully tracked volume (right). The prediction model was trained on a Gulf of Mexico dataset. Copyright of the authors and EAGE, and used under a Fair Use claim.

Secret horizon tracker

Horizons tracked with Figueiredo et al's machine learning algorithm. The horizons correctly capture the discontinuities. Copyright of the authors and EAGE. Used under a Fair Use claim.

Horizons tracked with Figueiredo et al's machine learning algorithm. The horizons correctly capture the discontinuities. Copyright of the authors and EAGE. Used under a Fair Use claim.

The most substantial piece of machine learning I saw was Eduardo Figueiredo from Pontifical Catholic University in Rio, in the same session as Waldeland. He's using a neural net called Growing Neural Gas to classify (aka or 'label') the input data in a number of different ways. This training step takes a little time. The label sets can now be compared to decide on the similarity between two samples, based on the number of labels the samples have in common but also including a comparison to the original seed, which essentially acts as a sort of brake to stop things running away. This progresses the pick. If a decision can't be reached, a new global seed is selected randomly. If that doesn't work, picking stops. Unfortunately he did not show a comparison to an ordinary autotracker, either in terms of time or quality, but the results did look quite good. The work was done 'in cooperation with Petrobras', so it's not surprising the code is not available. I was a bit surprised that Figueiredo was even unable to share any details of the implementation.

More on interpretation

The other two interesting talks in the session were two from Paul de Groot (dGB Earth Sciences) and Gaynor Paton (GeoTeric). Paul introduced the new Thalweg Tracker in OpendTect — the only piece of software from the session that you can actually run, albeit for a fee — which is a sort of conservative voxel tracker. Unsurprisingly, Paul was also very thorough with his examples, and his talk served as a tutorial in how to make use of, and give attribution to, open data. (I'm nearly done with the grumbling about openness for now, I promise, but I can't help mentioning that I find it a bit ironic that those scientists unwilling to share their work are also often a bit lax with giving credit to others whose work they depend on.)

Gaynor's talk was about colour, which you may know we enjoy thinking about. She had gathered 24 seismic interpreters, five of whom had some form of colour deficiency. She gave the group some interpretation tasks, and tried to gauge their performance in the tasks. It seemed interesting enough, and I immediately wondered if we could help out with Pick This, especially to help grow the sample size, and by blinding the study. But the conclusion seemed to be that, if there are ways in which colour blind interpreters are less capable at image interpretation, for example where hue is important, they compensate for it by interpreting other aspects, such as contrast and shape. 

Paton's research into how colour deficient people interpret attributes. There were 5 colour deficient subjects and 19 colour normal. The colour deficient subjects were more senstive to subtle changes in saturation and to feature shapes. Image copyright Paton and EAGE, and used here under a fair use claim.

Paton's research into how colour deficient people interpret attributes. There were 5 colour deficient subjects and 19 colour normal. The colour deficient subjects were more senstive to subtle changes in saturation and to feature shapes. Image copyright Paton and EAGE, and used here under a fair use claim.

That's it for now. I have a few other highlights to share; I'll try to get to them next week. There was a bit of buzz around the Seismic Apparition talks from ETHZ and Statoil, for example. If you were at the conference, I'd love to hear your highlights too, please share them in the comments.

References

A.U. Waldeland* (University of Oslo) & A.H.S. Solberg (University of Oslo). 3D Attributes and Classification of Salt Bodies on Unlabelled Datasets. 78th EAGE Conference & Exhibition 2016. DOI 10.3997/2214-4609.201600880. Available in EarthDoc.

M. Pelissier (Dagang Zhaodong Oil Company), C. Yu (Dagang Zhaodong Oil Company), R. Singh (dGB Earth Sciences), F. Qayyum (dGB Earth Sciences), P. de Groot* (dGB Earth Sciences) & V. Romanova (dGB Earth Sciences). Thalweg Tracker - A Voxel-based Auto-tracker to Map Channels and Associated Margins. 78th EAGE Conference & Exhibition 2016. DOI 10.3997/2214-4609.201600879. Available in EarthDoc. 

G. Paton* (GeoTeric). The Effect of Colour Blindness on Seismic Interpretation. 78th EAGE Conference & Exhibition 2016. DOI 10.3997/2214-4609.201600883. Available in EarthDoc.

A.M. Figueiredo* (Tecgraf / PUC-Rio), J.P. Peçanha (Tecgraf / PUC-Rio), G.M. Faustino (Tecgraf / PUC-Rio), P.M. Silva (Tecgraf / PUC-Rio) & M. Gattass (Tecgraf / PUC-Rio). High Quality Horizon Mapping Using Clustering Algorithms. 78th EAGE Conference & Exhibition 2016. DOI 10.3997/2214-4609.201600878. Available in EarthDoc.

Open source FWI, I mean geoscience

I'm being a little cheeky. Yesterday's Open Source Geoscience workshop at EAGE was not really only about full waveform inversion (FWI). True, it was mostly about geophysics, but there was quite a bit of new stuff too.

But there was quite a bit on FWI.

The session echoed previous EAGE sessions on the same subject in 2006 and 2012, and was chaired by Filippo Broggini (of ETH Zürich), Sergey Fomel (University of Texas), Thomas Günther (LIAG Hannover), and Russell Hewett (Total, unfortunately not present). It started with a look at core projects like Madagascar and OpendTect. There were some (for me) pretty hard core, mathematics-heavy contributions. And we got a tour of some new and newish projects that are seeking users and/or contributors. Rather than attempting to cover everything, I'm going to exercise my (biased and ill-gotten) judgment and focus on some highlights from the day.

Filippo Broggini started by reminding us of why Joe Dellinger (BP) started this recurrent workshop a decade ago. Here's how Joe framed the value of open source to our community:

The economic benefits of a collaborative open-source exploration and production processing and research software environment would be enormous. Skilled geophysicists could spend more of their time doing innovative geophysics instead of mediocre computer science. Technical advances could be quickly shared and reproduced instead of laboriously re-invented and reverse-engineered. Oil companies, contractors, academics, and individuals would all benefit.

Did I mention that he wrote that 10 years ago?

Lessons learned from the core projects

Kristofer Tingdahl (dGB) then gave the view from his role as CEO of dGB Earth Sciences, the company behind OpendTect, the free and open source geoscience interpretation tool. He did a great job of balancing the good (their thousands of users, and their SEG Distinguished Achievement Award 2016) with the less good (the difficulty of building a developer community, and the struggle to get beyond only hundreds of paying users). His great optimism and natural business instinct filled us all with hope.

The irrepressible Sergey Fomel summed up 10 years of Madagascar's rise. In the journey from v0.9 to v2.0, the projects has moved from SourceForge to GitHub, gone from 6 to 72 developers, jumped from 30 to 260 reproducible papers, and been downloaded over 40 000 times. He also shared the story of his graduate experience at Stanford, where he was involved in building the first 'reproducible science' system with Jon Claerbout in the early 1990s. Un/fortunately, it turned out to be unreproducible, so he had to build Madagascar.

It's not (yet?) a core project, but John Stockwell (Colorado School of Mines) talked about OpenSeaSeis and barely mentioned SeismicUnix. This excellent little seismic processing project is now owned by CSM, after its creator, Bjoern Olofsson, had to give it up when he went to work for a corporation (makes sense, right? o_O ). The tool includes SeaView, a standalone SEGY viewer, as well as a graphical processing flow composer called XSeaSeis. IT prides itself on its uber-simple architecture (below). Want a gain step? Write gain.so and you're done. Perfect for beginners.

Jeffrey Shragge (UWA), Bob Clapp (SEP), and Bill Symes (Rice) provided some perspective from groups solving big math problems with big computers. Jeff talked about coaxing Madgascar — or M8R as the cool kids apparently refer to it — into the cloud, where it can chomp through 100 million core hours without setting tings on fire. This is a way for small enterprises and small (underfunded) research teams to get big things done. Bob told us about a nifty-looking HTML5 viewer for subsurface data... which I can't find anywhere. And Bill talked about 'mathematical fidelty'. and its application to solving large, expensive problems without creating a lot of intermediate data. His message: the mathematics should provide the API.

New open source tools in geoscience

The standout of the afternoon for me was University of Vienna post-doc Eun Young Lee's talk about BasinVis. The only MATLAB code we saw — so not truly open source, though it might be adapted to GNU Octave — and the only strictly geological package of the day. To support her research, Eun Young has built a MATLAB application for basin analysis, complete with a GUI and some nice visuals. This one shows a geological surface, gridded in the tool, with a thickness map projected onto the 'floor' of the scene:

I'm poorly equipped to write much about the other projects we heard about. For the record and to save you a click, here's the list [with notes] from my 'look ahead' post:

  • SES3D [presented by Alexey Gokhberg], a package from ETHZ for seismic modeling and inversion.
  • OpenFOAM [Gérald Debenest], a new open source toolbox for fluid mechanics.
  • PyGIMLi [Carsten Rücker], a geophysical modeling and inversion package.
  • PySIT [Laurent Demanet], the Python seismic imaging toolbox that Russell Hewett started while at MIT.
  • Seismic.jl [Nasser Kazemi] and jInv [Eldad Haber], two [modeling and inversion] Julia packages.

My perception is that there is a substantial amount of overlap between all of these packages except OpenFOAM. If you're into FWI you're spoilt for choice. Several of these projects are at the heart of industry consortiums, so it's a way for corporations to sponsor open source projects, which is awesome. However, most of them said they have closed-source components which only the consortium members get access to, so clearly the messaging around open source — the point being to accelerate innovation, reduce bugs, and increase value for everyone — is missing somewhere. There's still this idea that secrecy begets advantage begets profit, but this idea is wrong. Hopefully the other stuff, which may or may not be awesome, gets out eventually.


I gave a talk at the end of the day, about ways I think we can get better at this 'openness' thing, whatever it is. I will write about that some time soon, but in the meantime you're welcome to see my slides here.

Finally, a little time — two half-hour slots — was set aside for discussion. I'll have a go at summing that up in another post. Stay tuned!

BasinVis image © 2016 Eun Young Lee, used with permission. OpenSeaSeis image © 2016 Center for Wave Phenomena

READY PLAYER 1

The Subsurface Hackathon 2016 is over! Seventeen hackers gathered for the weekend at Impact HUB Vienna — an awesome venue and coworking space — and built geoscience-based games. I think it was the first geoscience hackathon in Europe, and I know it was the first time a bunch of geoscientists have tried to build games for each other in a weekend.

What went on 

The format of the event was the same as previous events: gather on Saturday, imagine up some projects, start building them by about 11 am, and work on them until Sunday at 4. Then some demos and a celebration of how amazingly well things worked out. All interspersed with coffee, food, and some socializing. And a few involuntary whoops of success.

What we made

The projects were all wonderful, but in different ways. Here's a quick look at what people built:

  • Trap-tris — a group of lively students from the University of Leeds and the Technical University of Denmark built a version of Tetris that creates a dynamic basin model. 
  • Flappy Seismic — another University of Leeds student, one from Imperial College, and a developer from Roxar, built a Flappy Bird inspired seismic interpretation game.
  • DiamonChaser (sic) — a team of devs from Giga Infosystems in Freiberg built a very cool drilling simulation game (from a real geomodel) aimed at young people.
  • Guess What — a developer from Spain and two students from UNICAMP in Brazil built a 'guess the reflection coefficient' game for inverting seismic.

I will write up the projects properly in a week or two (this time I promise :) so you can see some screenshots and links to repos and so on... but for now here are some more pictures of the event.

The fun this year was generously sponsored by EMC. David Holmes, the company's CTO (Energy), spent his weekend hanging out at the venue, graciously mentoring the teams and helping to provide some perspective or context, and help carrying pizza boxes through the streets of Vienna, when it was needed.


Click on the hackathon tag below to read about previous hackathons