Pick This! Social interpretation

PIck This is a new web app for social image interpretation. Sort of Stack Exchange or Quora (both awesome Q&A sites) meets Flickr. You look for an interesting image and offer your interpretation with a quick drawing. Interpretations earn reputation points. Once you have enough rep, you can upload images and invite others to interpret them. Find out how others would outline that subtle brain tumour on the MRI, or pick that bifurcated fault...

A section from the Penobscot 3D, offshore Nova Scotia, Canada. Overlain on the seismic image is a heatmap of interpretations of the main fault by 26 different interpreters. The distribution of interpretations prompts questions about what is 'the' answer. Pick this image yourself at pickthis.io.

The app was born at the Geophysics Hackathon in Denver last year. The original team consisted of Ben Bougher, a UBC student and long-time Agile collaborator, Jacob Foshee, a co-founder of Durwella, Chris Chalcraft, a geoscientist at OpenGeoSolutions, Agile's own Evan Bianco of course, and me ordering pizzas and googling domain names. By demo time on Sunday afternoon, we had a rough prototype, good enough for the audience to provide the first seismic interpretations.

Getting from prototype to release

After the hackathon, we were very excited about Pick This, with lots of ideas for new features. We wanted it to be easy to upload an image, being clear about its provenance, and extremely easy to make an interpretation, right in the browser. After some great progress, we ran into trouble bending the drawing library, Raphael.js, to our will. The app languished until Steve Purves, an affable geoscientist–programmer who lives on a volcano in the middle of the Atlantic, came to the rescue a few days ago. Now we have something you can use, and it's fun! For example, how would you pick this unconformity? 

This data is proprietary to MultiKlient Invest AS. Licensed CC-BY-SA. 

This beautiful section is part of this month's Tutorial in SEG's The Leading Edge magazine, and was the original inspiration for the app. The open access essay is by Don Herron, the creator of Interpreter Sam, and describes his approach to interpreting unconformities, using this image as the partially worked example. We wanted a way for readers to try the interpretation themselves, without having to download anything — it's always good to have a use case before building something new. 

What's next for Pick This?

I'm really excited about the possibilities ahead. Apart from the fun of interpreting other people's data, I'm especially excited about what we could learn from the tool — how long do people spend interpreting? How many edits do they make before submitting? And we'd love to add other modes to the tool, like choosing between two image enhancement results, or picking multiple features. And these possibilities only multiply when you think about applications outside earth science, in medical imaging, remote sensing, or astronomy. So much to do, so little time! 

We trust your opinion. Maybe you can help us:

• Is Pick This at all interesting or fun or useful to you? Is there a use case that occurs to you? 
• Making the app better will take time and therefore money. If your organization is interested in image enhancement, subjectivity in interpretation, or machine learning, then maybe we can work together. Get in touch!

Whatever you do, please have a look at Pick This and let us know what you think.

The new open geophysics tools

The hackathon in Denver was more than 6 weeks ago. I kept thinking, "Oh, I must post a review of what went down" (beyond the quick wrap-up I did at the time), but while I'm a firm believer in procrastination six weeks seems unreasonable... Maybe it's taken this long to scrub down to the lasting lessons. Before those, I want to tell you who the teams were, what they did, and where you can find their (100% open source!) stuff. Enjoy!

Geophys Wiz

Andrew Pethick, Josh Poirier, Colton Kohnke, Katerina Gonzales, and Elijah Thomas — GitHub repo

This team had no trouble coming up with ideas — perhaps a reflection of their composition, which was more heterogeneous than the other teams. Josh is at NEOS, the consulting and software firm, and Andrew is a postdoc at Curtin in Perth, Australia, while the other 3 are students at Mines. The team eventually settled on building MT Black Box, a magnetotellurics modeling web application. 

Last thing: Don't miss Andrew Pethick's write-up of the event. 

Seemingly Concerned Neighbours

Elias Arias, Brent Putman, Thomas Rapstine, and Gabriel Martinez — Github repo

These four young geophysicists from the Colorado School of Mines impressed everyone with their work ethic. Their tight-knit team came in with a plan, and proceeded to scribble up the coolest-looking whiteboard of the weekend. After learning some Android development skills 'earlier this week', they pulled together a great little app for forward modeling magnetotelluric responses. 

Well tie guys

Michaël Montouchet, Graham Dawes, Mark Roberts

It was terrific to have pro coders Graham and Michaël with us — they flew from the UK to be with us, thanks to their employer and generous sponsor ffA GeoTeric. They hooked up with Mark, a Denver geophysicist and developer, and hacked on a well-tie web application, rightly identifying a gap in the open source market, so to speak (there is precious little out there for well-based workflows). They may have bitten off more than they could chew in just 2 days, so I hope we can get together with them again to finish it off. Who's up for a European hackathon? 

Five hour wonders

Rowan Cockett and Seogi Kang — GitHub repo for SimPEG

These two characters from UBC didn't get going till Sunday morning, but in just five hours they built a sweet web app for forward modeling the DC resistivity response of a buried disk. They weren't starting from scratch, because Rowan and others have spent months honing SimPEG, a rich open-source geophysical library, but minds were nonetheless blown.

Key takeaway: interactivity beyond sliders for the win.

Pick This!

Ben Bougher, Jacob Foshee, Evan Bianco, and an immiscible mixture of Chris Chalcraft and me — GitHub repo

Wouldn't you sometimes like to know how other people would interpret the section you're working on? This team, a reprise of the dream team from Houston in 2013, built a simple way to share images and invite others to interpret them. When someone has completed their interpretation, only then do they get to see the ensemble — everyone else's interpretations — in a heatmap. Not only did this team demo live software at pickthis.io, but the audience provided the first crowdsourced picks in real time. 

We'll be blogging more about Pick This soon. We're actively seeking ideas, images, interpreters, and financial support. Keep an eye out.

What I learned at this hackathon

• Potential fields are an actual thing! OK, kidding, but three out of five teams built potential field modeling tools. I wasn't expecting that, and I think the judges were impressed at the breadth. 
• 30 hours is easily enough time to build something pretty cool. Heck, 5 hours is enough if you're made of the right stuff. 
• Students can happily build prototypes alongside professional developers, and even teach them a thing or two. And vice versa. Are hackathons a leveller of playing fields?
• We need to remove the road blocks to more people enjoying this event. To help with this, next time there will be a 1-day bootcamp before the hackathon.
• After virtually doubling in size from 2013 to 2014, it's clear that the 2015 Hackathon in New Orleans is going to be awesome! Mark your calendar: 17 and 18 October 2015.

Thank you!

Thank you to the creative, energetic geophysicists that came. It was a privilege to meet and hack with you!

Thank you to the judges who gave up their Sunday teatime to watch the demos and give precious feedback to the teams: Steve Adcock, Jamie Allison, Maitri Erwin, Dennis Cooke, Chris Krohn, Shannon Bjarnason, David Holmes, and Tracy Stark. Amazing people, one and all.

A final Thank You to our sponsors — dGB Earth Sciences, ffA GeoTeric, and OpenGeoSolutions. You guys are totally awesome! Seriously.

The most epic geophysics hackathon in the world, ever

Words can't express how awesome the 2014 Geophysics Hackthon was. The spirit embodied by the participants is shared by our generous sponsors... the deliberate practice of creativity and collaboration. 

We convened at Thrive, a fantastic coworking space in the hip Lower Downtown district of Denver. Their friendly staff went well beyond their duty in accommodating our group. The abundance of eateries and bars makes it perfect for an event like this, especially when the organization is a bit, er, spontaneous.

We opened the doors at 8 on Saturday morning and put the coffee and breakfast out, without any firm idea of how many people would show up. But by 9 a sizeable cohort of undergrads and grad students from the Colorado School of Mines had already convened around projects, while others trickled in. The way these students showed up, took ownership, and rolled up their sleeves was inspiring. A few folks even spent last week learning Android in order to put their ideas on a mobile device. While at times we encounter examples that have caused us to wonder if we are going to be alright, these folks, with their audacity and wholesomeness, revive faith that we will. 

The theme of the event was resolution, but really the brief was wide open. There was a lot of non-seismic geophysics, a lot of interactive widgets ('slide this to change the thickness; slide that to change the resistivity'), and a lot of novel approaches. In a week or two we'll be posting a thorough review of the projects the 6 teams built, so stay tuned for that.

The photos are all on Flickr, or you can visit our Hashpi.pe for the captions and other tweetage.

Another great outcome was that all of the projects are open source. Several of the projects highlighted the escape-velocity innovation that is possible when you have an open platform behind you. The potential impact of tools like Mines JTK, SimPEG, and Madagascar is huge. Our community must not underestimate the super-powers these frameworks give us.

The hackathon will be back next year in New Orleans (17 and 18 October: mark your calendars!). We will find a way to add a hacker bootcamp for those wanting to get into this gig. And we're looking for ways to make something happen in Europe. If you have a bright idea about that, please get in touch. 

The hackathon is coming

The Geophysics Hackathon is one month away! Signing up is not mandatory — you can show up on the day if you like — but it does help with the planning. It's 100% free, and I guarantee you'll enjoy yourself. You'll also learn tons about geophysics and about building software. Deets: Thrive, Denver, 8 am, 25–26 October. Bring a laptop.

Need more? Here's all the info you could ask for. Even more? Ask by email or in the comments. 

Send your project ideas

The theme this year is RESOLUTION. Participants are encouraged to post projects to hackathon.io ahead of time — especially if you want to recruit others to help. And even if you're not coming to the event, we'd love to hear your project ideas. Here are some of the proto-ideas we have so far: 

• Compute likely spatial and temporal resolution from some basic acquisition info: source, design, etc.
• Do the same but from information from the stack: trace spacing, apparent bandwidth, etc.
• Find and connect literature about seismic and log resolution using online bibliographic data.
• What does the seismic spectrum look like, given STFT limitations, or Gabor uncertainty?

If you have a bright idea, get in touch by email or in the comments. We'd love to hear from you.

Thank you to our sponsors

Three forward-thinking companies have joined us in making the hackathon as much a geophysics party as well as a scientific workshop (a real workshop). I think this industry may have trained us to take event sponsorship for granted, but it's easy to throw $5000 at the Marriott for Yet Another Coffee Break. Handing over money to a random little company in Nova Scotia to buy coffee, tacos, and cool swag for hungry geophysicists and programmers takes real guts! 

Please take a minute to check out our sponsors and reward them for supporting innovation in our community. 

Students: we are offering $250 bursaries to anyone looking for help with travel or accommodation. Just drop me a line with a project idea. If you know a student that might enjoy the event, please forwadrd this to them.

The hack is back: An invitation to get creative

We're organizing another hackathon! It's free, and it's for everyone — not just programmers. So mark your calendar for the weekend of 25 and 26 October, sign up with a friend, and come to Denver for the most creative 48 hours you'll spend this year. Then stay for the annual geophysics fest that is the SEG Annual Meeting!

First things first: what is a hackathon? Don't worry, it's not illegal, and it has nothing to do with security. It has to do with ideas and collaborative tool creation. Here's a definition from Wikipedia:

A hackathon (also known as a hack day, hackfest, or codefest) is an event in which computer programmers and others involved in software development, including graphic designers, interface designers and project managers, collaborate intensively on software projects.

I would add that we just need a lot of scientists — you can bring your knowledge of workflows, attributes, wave theory, or rock physics. We need all of that.

Creativity in geophysics

The best thing we can do with our skills — and to acquire new ones — is create things. And if we create things with and alongside others, we learn from them and they learn from us, and we make lasting connections with people. We saw all this last year, when we built several new geophysics apps:

The event is at the THRIVE coworking space in downtown Denver, less than 20 minutes' walk from the convention centre — a Manhattan distance of under 1 mile. They are opening up especially for us — so we'll have the place to ourselves. Just us, our laptops, high-speed WiFi, and lots of tacos. 

Sign up here.It's going to be awesome.

The best in the biz

This business is blessed with some forward-looking companies that know all about innovation in subsurface geoscience. We're thrilled to have some of them as sponsors of our event, and I hope they will also be providing coders and judges for the event itself. So far we have generous support from dGB — creators of the OpendTect seismic interpretation platform — and ffA — creators the GeoTeric seismic attribute analysis toolbox. A massive Thank You to them both.

If you think your organization might be up for supporting the event, please get in touch! And remember, a fantastic way to support the event — for free! — is just to come along and take part. Sign your team up here!

Student grants

We know there's a lot going on at SEG on this same weekend, and we know it's easier to get money for traditional things like courses. So... We promise that this hackathon will bring you at least as much lasting joy, insight, and skill development as any course. And, if you'll write and tell us what you'd build, we'll consider you for one of four special grants of $250 to help cover your extra costs. No strings. Send your ideas to matt@agilegeoscience.com.

Update

on 2014-09-07 12:17 by Matt Hall

OpenGeoSolutions, the Calgary-based tech company that's carrying the FreeUSP torch and exporing the frequency domain so thoroughly, has sponsred the hackathon again this year. Thank you to Jamie and Chris and everyone else at OGS!

Mining innovation

by Jelena Markov and Tom Horrocks

Jelena is a postgraduate student and Tom is a research assistant at the University of Western Australia, Perth. They competed in the recent RIIT Unearthed hackathon, and kindly offered to tell us all about it. Thank you, Jelena and Tom!

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Two weeks ago Perth coworking space Spacecubed hosted a unique 54-hour-long hackathon focused on the mining industry. Most innovations in the mining industry are the result of long-term strategic planning in big mining companies, or collaboration with university groups. In contrast, the Unearthed hackathon provided different perspectives on problems in the mining domain by giving 'outsiders' a chance to work on industry problems.

The event attracted web-designers, software developers, data gurus, and few geology and geophysics geeks, all of whom worked together on data — both open and proprietary from the Western Australian Government and industry respectively — to deliver time-constrained solutions to problems in the mining domain. There were around 100 competitors divided into 18 teams, but just one underlying question: can web-designers and software developers create solutions that compete, on an innovative level, with those from the R&D divisions of mining companies? Well, according to panel of mining executives and entrepreneurs, they can.

Safe, seamless shutdown

The majority of the teams chose to work on logistic problems in mining production. For example, the Stockphiles worked on a Rio Tinto problem about how to efficiently and safely shut down equipment without majorly disturbing the overall system. Their solution used Directed Acyclic Graphs as the basis for an interactive web-based interface that visualised the impacted parts of the system. Outside of the mining production domain, however, two teams tackled problems focused on geology and geophysics...

Geoscience hacking

The team Ultramafia used augmented reality and cloud-based analysis to visualize geological mapping, with the underlying theme of the smartphone replacing the geological hammer, and also the boring task of joint logging!

The other team in this domain — and the team we were part of — was 50 Grades of Shale...

The team consisted of three PhD students and three staff members from the Centre for Exploration Targeting at the UWA. We created an app for real-time downhole petrophysical data analysis — dubbed Wireline Spelunker — that automatically classifies lithology types from wireline logs and correlates user-selected log segments across the drill holes. We used some public libraries for machine learning and signal analysis algorithms, and within 54 hours the team had implemented a workflow and interface, using data from the government database.

The boulder detection problem

The first prize, a 1 oz gold medal, was awarded to Applied Mathematics, who came up with an extraordinary use of accelerometers. They worked on Rio Tinto's 'boulder detection' problem — early detection of a large rocks loaded into mining trucks in order to prevent crusher malfunctions later in the process, which could ultimately cost $250,000 per hour in lost revenue. The team's solution was to detect large boulders by measuring the truck's vibrations during loading.

Second and third prizes went to Pit IQ and The Froys respectively. Both teams worked on data visualization problems on the mine site, and came up with interactive mobile dashboards.

A new role for Perth?

Besides having a chance to tackle problems that are costing the mining industry millions of dollars a year, this event has demonstrated that Perth is not just a mining hub but also has potential for something else.

This potential is recognized by event organizers Resources Innovation through Information Technology — Zane, Justin, Paul, and Kevin. They see potential in Perth as a centre for tech start-ups focused on the resource industry. Evidently, the potential is huge.

Follow Jelena on Twitter

Hacking logs

Over the weekend, 6 intrepid geologist-geeks gathered in a coworking space in the East Downtown area of Houston. With only six people, I wasn't sure we could generate the same kind of creative buzz we had at the geophysics hackathon last September. But sitting with other geoscientists and solving problems with code works at any scale. 

The theme of the event was 'Doing cool things with log data'. There were no formal teams and no judging round. Nonetheless, some paired up in loose alliances, according to their interests. Here's a taste of what we got done in 2 days...

Multi-scale display

Jacob Foshee and Ben Bougher worked on some JavaScript to display logs with the sort of adaptive scrolling feature you often see on finance sites for displaying time series. The challenge was to display not just one log with its zoomed version, but multiple logs at multiple scales — and ideally core photos too. They got the multiple logs, though not yet at multiple scales, and they got the core photo. The example (right) shows some real logs from Panuke, a real core photo from the McMurray, and a fake synthetic seismogram. 

Click on the image for a demo. And the code is all open, all the way. Thanks guys for an awesome effort!

Multi-scale log attributes

Evan and Mark Dahl (ConocoPhillips) — who was new to Python on Friday — built some fascinating displays (right). The idea was to explore stratigraphic stacking patterns in scale space. It's a little like spectral decomposition for 1D data. They averaged a log at a range of window sizes, increasing exponentially (musicians and geophysicists know that scale is best thought of in octaves). Then they made a display that ranges from short windows on the left-hand side to long ones on the right. Once you get your head around what exactly you're looking at here, you naturally want to ask questions about what these gothic-window patterns mean geologically (if anything), and what we can do with them. Can we use them to help train a facies classifier, for example? [Get Evan's code]

Facies from logs

In between running for tacos, I worked on computing grey-level co-occurence matrices (GLCMs) for logs, which are a prerequisite for computing certain texture attributes. Why would anyone do this? We'd often like to predict facies from well logs; maybe log textures (spiky vs flat, upwards-fining vs barrel-shaped) can help us discriminate facies better. [Download my IPython Notebook]

Wassim Benhallam (of Lisa Stright's Rocks to Models lab at University of Utah) worked on machine learning algorithms for computing facies from core. He started pursuing self-organizing maps as an interesting line of attack, and plans to use MATLAB to get something working. I hope he tells us how it goes!

We didn't have a formal contest at this event, but our friend Maitri Erwin was kind enough to stop by with some excellent wine and her characteristically insightful and inquisitive demeanour. After two days rattling around with nothing but geeks and tacos for company, she provided some much-needed objectivity and gave us all good ideas about how to develop our efforts in the coming weeks. 

We'll be doing this again in Denver this autumn, some time around the SEG Annual Meeting. If it appeals to your creativity — maybe there's a tool you've always wished for — why not plan to join us?  

As I get around to it, I'll be dumping more info and pictures over on the wiki. 

A long weekend of creative geoscience computing

The Rock Hack is in three weeks. If you're in Houston, for AAPG or otherwise, this is going to be a great opportunity to learn some new computer skills, build some tools, or just get some serious coding done. The Agile guys — me, Evan, and Ben — will be hanging out at START Houston, laptops open, all say 5 and 6 April, about 8:30 till 5. The breakfast burritos and beers are on us.

Unlike the geophysics hackathon last September, this won't be a contest. We're going to try a more relaxed, unstructured event. So don't be shy! If you've always wanted to try building something but don't know where to start, or just want to chat about The Next Big Thing in geoscience or technology — please drop in for an hour, or a day.

Here are some ideas we're kicking around for projects to work on:

• Sequence stratigraphy calibration app to tie events to absolute geologic time and to help interpret systems tracts.
• Wireline log 'attributes'.
• Automatic well-to-well correlation.
• Facies recognition from core.
• Automatic photomicrograph interpretation: grain size, porosity, sorting, and so on.
• A mobile app for finding and capturing data about outcrops.
• An open source basin modeling tool.

Short course

If you feel like a short course would get you started faster, then come along on Friday 4 April. Evan will be hosting a 1-day course, leading you through getting set up for learning Python, learning some syntax, and getting started on the path to scientific computing. You won't have super-powers by the end of the day, but you'll know how to get them.

The course includes food and drink, and lots of code to go off and play with. If you've always wanted to get started programming, this is your chance!

Rock Hack 2014

We're hosting another hackathon! This time, we're inviting geologists in all their colourful guises to come and help dream up cool tools, find new datasets, and build useful stuff. Mark your calendar: 5 & 6 April, right before AAPG.

On 4 April there's the added fun of a Creative geocomputing course. So you can learn some skills, then put them into practice right away. More on the course next week.

What's a hackathon?

It's not as scary — or as illegal — as it sounds! And it's not just for coders. It's just a roomful of creative geologists and friendly programmers figuring out two things together:

1. What tools would help us in our work?
2. How can we build those tools?

So for example, we might think about problems like these:

• A sequence stratigraphy calibration app to tie events to absolute geologic time
• Wireline log 'attributes'
• Automatic well-to-well correlation
• Facies recognition from core
• Automatic photomicrograph interpretation: grain size, porosity, sorting, and so on
• A mobile app for finding and capturing data about outcrops
• Sedimentation rate analysis, accounting for unconformities, compaction, and grain size

I bet you can think of something you'd like to build — add it to the list!

Still not sure? Check out what we did at the Geophysics Hackathon last autumn...

How do I sign up?

You can sign up for the creative geocomputing course at Eventbrite.

If you think Rock Hack sounds like a fun way to spend a weekend, please drop us a line or sign up at Hacker League. If you're not sure, please come anyway! We love visitors.

If you think you know someone who'd be up for it, let them know with the sharing buttons below.

The poster image is from an original work by Flickr user selkovjr.

October linkfest

From Hart (2013). ©SEG/AAPGIt's the Hallowe'en linkfest! Just the good bits from our radar...

If you're a member of SEG or AAPG, you can't have missed their new joint-venture journal, Interpretation. Issue 2 just came out. My favourite article so far has been Bruce Hart's Whither seismic stratigraphy in Issue 1. It included these excellent little forward models from an earlier paper of his — it's so important for interpreter's to think in this space where geological architecture and geophysical imaging overlap. 

Muon tomography is in the news again, this time in relation to monitoring CCS repositories (last time it was volcanos). Jon Gluyas, author of the textbook Petroleum Geoscience, is the investgator at Durham in the UK (my alma mater). I do love the concept — imaging the subsurface with cosmic rays — but I'm only just getting to grips with sound waves.

If you read this blog regularly, you probably have some geeky tendencies. We've linked to a couple of these blogs before, but they're must-read for anyone into technology and geoscience, with lots of code and workflow examples: 

• Zoltan Sylvester's Hindered Settling — code for sedimentologists!
• Darren Wilkinson's blog — ternary plots in R, anyone?
• Rob Simmon's Elegant Figures — as featured in our recent series on colour
• Leo Uieda's blog is one way to keep up with his awesome project, Fatiando a Terra

Continuing the geeky theme, we've been getting more and more into building things recently. Check out our fiddling in GitHub (a code repository) — an easy way in is code.agilegeoscience.com. Watch this space!

Speaking of fiddling with code, you already know about the hackathon we hosted in Houston last month. But there's talk of repeating the fun at the AAPG Annual Convention, also in Houston, in April next year. Brian Romans has started a list of potential projects around digital stratigraphy — please leave a comment there or here to add to it. Where's the gap in your workflow?

A few more quick hits:

• I recently did a Twitter interview with Northeastern University's College of Science
• Trowel Blazers did a Wikipedia editing event on Women in Geology (right)
• The Center for Wave Phenomena at Colorado School of Mines has a YouTube channel. It features some pretty deep geophysical content.
• Surge Accelerator is looking for energy-related start-ups to fund in its next class. They have $30k and months of mentoring for the winners.

If you want these nuggets fresh, you can follow me on Twitter or glance at my pinboard. If you have stuff to share, use the comments or get in touch. Over and out.

Seismic models: Hart, BS (2013). Whither seismic stratigraphy? Interpretation, volume 1 (1), and is copyright of SEG and AAPG. The image from the Trowel Blazers event is licensed CC-BY-SA by Wikipedia user Mrjohncummings.