A long weekend of creative geoscience computing

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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.

Eventbrite - Agile Geocomputing

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!

Creating in the classroom

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The day before the Atlantic Geoscience Colloquium, I hosted a one-day workshop on geoscience computing to 26 maritime geoscientists. This was my third time running this course. Each time it has needed tailoring and new exercises to suit the crowd; a room full of signal-processing seismologists has a different set of familiarities than one packed with hydrologists, petrologists, and cartographers. 

Easier to consume than create

At the start of the day, I asked people to write down the top five things they spend time doing with computers. I wanted a record of the tools people use, but also to take collective stock of our creative, as opposed to consumptive, work patterns. Here's the result (right).

My assertion was that even technical people spend most of their time in relatively passive acts of consumption — browsing, emailing, and so on. Creative acts like writing, drawing, or using software were in the minority, and only a small sliver of time is spent programming. Instead of filing into a darkened room and listening to PowerPoint slides, or copying lectures notes from a chalkboard, this course was going to be different. Participation mandatory.

My goal is not to turn every geoscientist into a software developer, but to better our capacity to communicate with computers. Giving people resources and training to master this medium that warrants a new kind of creative expression. Through coaching, tutorials, and exercises, we can support and encourage each other in more powerful ways of thinking. Moreover, we can accelerate learning, and demystify computer programming by deliberately designing exercises that are familiar and relevant to geoscientists. 

Scientific computing

In the first few hours students learned about syntax, built-in functions, how and why to define and call functions, as well as how to tap into external code libraries and documentation. Scientific computing is not necessarily about algorithm theory, passing unit tests, or designing better user experiences. Scientists are above all interested in data, and data processes, helped along by rich graphical displays for story telling.

Elevation model (left), and slope magnitude (right), Cape Breton, Nova Scotia. Click to enlarge.

In the final exercise of the afternoon, students produced a topography map of Nova Scotia (above left) from a georeferenced tiff. Sure, it's the kind of thing that can be done with a GIS, and that is precisely the point. We also computed some statistical properties to answer questions like, "what is the average elevation of the province?", or "what is the steepest part of the province?". Students learned about doing calculus on surfaces as well as plotting their results. 

Programming is a learnable skill through deliberate practice. What's more, if there is one thing you can teach yourself on the internet, it is computer programming. Perhaps what is scarce though, is finding the time to commit to a training regimen. It's rare that any busy student or working professional can set aside a chunk of 8 hours to engage in some deliberate coaching and practice. A huge bonus is to do it alongside a cohort of like-minded individuals willing and motivated to endure the same graft. This is why we're so excited to offer this experience — the time, help, and support to get on with it.

How can I take the course?

We've scheduled two more episodes for the spring, conveniently aligned with the 2014 AAPG convention in Houston, and the 2014 CSPG / CSEG convention in Calgary. It would be great to see you there!

Eventbrite - Agile Geocomputing  Eventbrite - Agile Geocomputing

Or maybe a customized in-house course would suit your needs better? We'd love to help. Get in touch.

To plot a wavelet

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As I mentioned last time, a good starting point for geophysical computing is to write a mathematical function describing a seismic pulse. The IPython Notebook is designed to be used seamlessly with Matplotlib, which is nice because we can throw our function on graph and see if we were right. When you start your own notebook, type

ipython notebook --pylab inline

We'll make use of a few functions within NumPy, a workhorse to do the computational heavy-lifting, and Matplotlib, a plotting library.

import numpy as np
import matplotlib.pyplot as plt

Next, we can write some code that defines a function called ricker. It computes a Ricker wavelet for a range of discrete time-values t and dominant frequencies, f:

def ricker(f, length=0.512, dt=0.001):
    t = np.linspace(-length/2, (length-dt)/2, length/dt)
    y = (1.-2.*(np.pi**2)*(f**2)*(t**2))*np.exp(-(np.pi**2)*(f**2)*(t**2))
    return t, y

Here the function needs 3 input parameters; frequency, f, the length of time over which we want it to be defined, and the sample rate of the signal, dt. Calling the function returns two arrays, the time axis t, and the value of the function, y.

To create a 5 Hz Ricker wavelet, assign the value of 5 to the variable f, and pass it into the function like so,

f = 5
t, y = ricker (f)

To plot the result,

plt.plot(t, y)

But with a few more commands, we can improve the cosmetics,

plt.figure(figsize=(7,4))
plt.plot( t, y, lw=2, color='black', alpha=0.5)
plt.fill_between(t, y, 0,  y > 0.0, interpolate=False, hold=True, color='blue', alpha = 0.5)
plt.fill_between(t, y, 0, y < 0.0, interpolate=False, hold=True, color='red', alpha = 0.5)

# Axes configuration and settings (optional)
plt.title('%d Hz Ricker wavelet' %f, fontsize = 16 )
plt.xlabel( 'two-way time (s)', fontsize = 14)
plt.ylabel('amplitude', fontsize = 14)
plt.ylim((-1.1,1.1))
plt.xlim((min(t),max(t)))
plt.grid()
plt.show()

Next up, we'll make this wavelet interact with a model of the earth using some math. Let me know if you get this up and running on your own.

Let's do it

It's short notice, but I'll be in Calgary again early in the new year, and I will be running a one-day version of this new course. To start building your own tools, pick a date and sign up:

Eventbrite - Agile Geocomputing    Eventbrite - Agile Geocomputing

Coding to tell stories

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Last week, I was in Calgary on family business, but I took an afternoon to host a 'private beta' for a short course that I am creating for geoscience computing. I invited about twelve familiar faces who would be provide gentle and constuctive feedback. In the end, thirteen geophysicists turned up, seven of whom I hadn't met before. So much for familiarity.

I spent about two and half hours stepping through the basics of the Python programming language, which I consider essential material — getting set up with Python via Enthought Canopy, basic syntax, and so on. In the last hour of the afternoon, I steamed through a number of geoscientific examples to showcase exercises for this would-be course. 

Here are three that went over well. Next week, I'll reveal the code for making these images. I might even have a go at converting some of my teaching materials from IPython Notebook to HTML:

To plot a wavelet

The Ricker wavelet is a simple analytic function that is used throughout seismology. This curvaceous waveform is easily described by a single variable, the dominant frequency of its many contituents frequencies. Every geophysicist and their cat should know how to plot one: 

To make a wedge

Once you can build a wavelet, the next step is to make that wavelet interact with the earth. The convolution of the wavelet with this 3-layer impedance model yields a synthetic seismogram suitable for calibrating seismic signals to subtle stratigraphic geometries. Every interpreter should know how to build a wedge, with site-specific estimates of wavelet shape and impedance contrasts. Wedge models are important in all instances of dipping and truncated layers at or below the limit of seismic resolution. So basically they are useful all of the time. 

To make a 3D viewer

The capacity of Python to create stunning graphical displays with merely a few (thoughtful) lines of code seemed to resonate with people. But make no mistake, it is not easy to wade through the hundreds of function arguments to access this power and richness. It takes practice. It appears to me that practicing and training to search for and then read documentation, is the bridge that carries people from the mundane to the empowered.

This dry-run suggested to me that there are at least two markets for training here. One is a place for showing what's possible — "Here's what we can do, now let’s go and build it". The other, more arduous path is the coaching, support, and resources to motivate students through the hard graft that follows. The former is centered on problem solving, the latter is on problem finding, where the work and creativity and sweat is. 

Would you take this course? What would you want to learn? What problem would you bring to solve?

Back to school

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My children go back to school this week. One daughter is going into Grade 4, another is starting kindergarten, and my son is starting pre-school at the local Steiner school. Exciting times.

I go all misty-eyed at this time of year. I absolutely loved school. Mostly the learning part. I realize now there are lots of things I was never taught (anything to do with computers, anything to do with innovation or entrepreneurship, anything to do with blogging), but what we did cover, I loved. I'm not even sure it's learning I like so much — my retention of facts and even concepts is actually quite bad — it's the process of studying.

Lifelong learning

Naturally, the idea of studying now, as a grown-up and professional, appeals to me. But I stopped tracking courses I've taken years ago, and actually now have stopped doing them, because most of them are not very good. I've found many successful (that is, long running) industry courses to be disappointingly bad — long-running course often seems to mean getting a tired instructor and dated materials for your $500 per day. (Sure, you said the course was good when you sis the assessment, but what did you think a week later? A month, a year later? If you even remember it.) I imagine it's all part of the 'grumpy old man' phase I seem to have reached when I hit 40.

But I am grumpy no longer! Because awesome courses are back...

So many courses

Last year Evan and I took three high quality, and completely free, massive online open courses, or MOOCs:

There aren't a lot of courses out there for earth scientists yet. If you're looking for something specific, RedHoop is a good way to scan everything at once.

The future

These are the gold rush days, the exciting claim-staking pioneer days, of massive online open courses. Some trends:

There are new and profound opportunities here for everyone from high school students to postgraduates, and from young professionals to new retirees. Whether you're into teaching, or learning, or both, I recommend trying a MOOC or two, and asking yourself what the future of education and training looks like in your world.

The questions is, what will you try first? Is there a dream course you're looking for?

Dream geoscience courses

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MOOCs mean it's never been easier to learn something new.This is an appeal for opinions. Please share your experiences and points of view in the comments.

Are you planning to take any technical courses this year? Are you satisfied with the range of courses offered by your company, or the technical societies, or the commercial training houses (PetroSkills, Nautilus, and so on)? And how do you choose which ones to take — do you just pick what you fancy, seek recommendations, or simply aim for field classes at low latitudes?

At the end of 2012, several geobloggers wrote about courses they'd like to take. Some of them sounded excellent to me too... which of these would you take a week off work for?

Here's my own list, complete with instructors. It includes some of the same themes...

  • Programming for geoscientists (learn to program!) — Eric Jones
  • Solving hard problems about the earth — hm, that's a tough one... Bill Goodway?
  • Communicating rocks online — Brian Romans or Maitri Erwin
  • Data-driven graphics in geoscience — the figure editor at Nature Geoscience
  • Mathematics clinic for geoscientists — Brian Russell
  • Becoming a GIS ninja — er, a GIS ninja
  • Working for yourself — needs multiple points of view
What do you think? What's your dream course? Who would teach it?

News of the month

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The last news of the year. Here's what caught our eye in December.

Online learning, at a price

There was an online university revolution in 2012 — look for Udacity (our favourite), Coursera, edX, and others. Paradigm, often early to market with good new ideas, launched the Paradigm Online University this month. It's a great idea — but the access arrangement is the usual boring oil-patch story: only customers have access, and they must pay $150/hour — more than most classroom- and field-based courses! Imagine the value-add if it was open to all, or free to customers.

Android apps on your PC

BlueStacks is a remarkable new app for Windows and Mac that allows you to run Google's Android operating system on the desktop. This is potentially awesome news — there are over 500,000 apps on this platform. But it's only potentially awesome because it's still a bit... quirky. I tried running our Volume* and AVO* apps on my Mac and they do work, but they look rubbish. Doubtless the technology will evolve rapidly — watch this space. 

2PFLOPS HPC 4 BP

In March, we mentioned Total's new supercomputer, delivering 2.3 petaflops (quadrillion floating point operations per second). Now BP is building something comparable in Houston, aiming for 2 petaflops and 536 terabytes of RAM. To build it, the company has allocated 0.1 gigadollars to high-performance computing over the next 5 years.

Haralick textures for everyone

Matt wrote about OpendTect's new texture attributes just before Christmas, but the news is so exciting that we wanted to mention it again. It's exciting because Haralick textures are among the most interesting and powerful of multi-trace attributes — right up there with coherency and curvature. Their appearance in the free and open-source core of OpendTect is great news for interpreters.

That's it for 2012... see you in 2013! Happy New Year.

This regular news feature is for information only. We aren't connected with any of these organizations, and don't necessarily endorse their products or services. Except OpendTect, which we definitely do endorse.

Journalists are scientists

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Tim Radford. Image: Stevyn Colgan.On Thursday I visited The Guardian’s beautiful offices in King’s Cross for one of their Masterclass sessions. Many of them have sold out, but Tim Radford’s science writing evening did so in hours, and the hundred-or-so budding writers present were palpably excited to be there. The newspaper is one of the most progressive news outlets in the world, and boasts many venerable alumni (John Maddox and John Durant among them). It was a pleasure just to wander around the building with a glass of wine, with some of London’s most eloquent nerds.

Radford is not a trained scientist, but a pure journalist. He left school at 16, idolized Dylan Thomas, joined a paper, wrote like hell, and sat on almost every desk before mostly retiring from The Guardian in 2005. He has won four awards from the Association of British Science Writers. More people read any one of his science articles on a random Tuesday morning over breakfast than will ever read anything I ever write. Tim Radford is, according to Ed Yong, the Yoda of science writers.

Within about 30 minutes it became clear what it means to be a skilled writer: Radford’s real craft is story-telling. He is completely at home addressing a crowd of scientists — he knows how to hold a mirror up to the geeks and reflect the fun, fascinating, world-changing awesomeness back at them. “It’s a terrible mistake to think that because you know about a subject you are equipped to write about it,” he told us, getting at how hard it is to see something from within. It might be easier to write creatively, and with due wonder, about fields outside our own.

Some in the audience weren’t content with being entertained by Radford, watching him in action as it were, preferring instead to dwell on controversy. He mostly swatted them aside, perfectly pleasantly, but one thing he was having none of was the supposed divide between scientists and journalists. Indeed, Radford asserted that journalists and scientists do basically the same thing: imagine a story (hypothesis), ask questions (do experiments), form a coherent story (theory) from the results, and publish. Journalists are scientists. Kind of.

I loved Radford's committed and unapologetic pragmatism, presumably the result of several decades of deadlines. “You don’t have to be ever so clever, you just have to be ever so quick,” and as a sort of corollary: “You can’t be perfectly right, but you must be mostly right.” One questioner accused journalists of sensationalising science (yawn). “Of course we do!” he said — because he wants his story in the paper, and he wants people to read it. Specifically, he wants people who don’t read science stories to read it. After all, writing for other people is all about giving them a sensation of one kind or another.

I got so much out of the 3 hours I could write at least another 2000 words, but I won’t. The evening was so popular that the paper decided to record the event and experiment with a pay-per-view video, so you can get all the goodness yourself. If you want more Radford wisdom, his Manifesto for the simple scribe is a must-read for anyone who writes.

Tim Radford's most recent book, The Address Book: Our Place in the Scheme of Things, came out in spring 2011.

The photograph of Tim Radford, at The World's Most Improbable Event on 30 September, is copyright of Stevyn Colgan, and used with his gracious permission. You should read his blog, Colganology. The photograph of King's Place, the Guardian's office building, is by flickr user Davide Simonetti, licensed CC-BY-NC.

News of the week

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Our regularly irregular news column returns! If you come across geoscience–tech tidbits, please drop us a line. 

A new wiki for geophysics

If you know Agile*, you know we like wikis, so this is big news. Very quietly, the SEG recently launched a new wiki, seeded with thousands of pages of content from Bob Sheriff's famous Encyclopedic Dictionary of Applied Geophysics. So far, it is not publicly editable, but the society is seeking contributors and editors, so if you're keen, get involved. 

On the subject of wikis, others are on the horizon: SPE and AAPG also have plans. Indeed members of SEG and AAPG were invited to take a survey on 'joint activities' this week. There's a clear opportunity for unity here — which was the original reason for starting our own subsurfwiki.org. The good news is that these systems are fully compatible, so whatever we build separately today can easily be integrated tomorrow. 

The DISC is coming

The SEG's Distinguished Instructor Short Course is in its 15th year and kicks off in 10 days in Brisbane. People rave about these courses, though I admit I felt like I'd been beaten about the head with the wave equation for seven hours after one of them (see if you can guess which one!). This year, the great Chris Liner (University of Houston prof and ex-editor of Geophysics) goes on the road with Elements of Seismic Dispersion: A somewhat practical guide to frequency-dependent phenomena. I'm desperate to attend, as frequency is one of my favourite subjects. You can view the latest schedule on Chris's awesome blog about geophysics, which you should bookmark immediately.

Broadband bionic eyes

Finally, a quirky story about human perception and bandwidth, both subjects close to Agile's core. Ex-US Air Force officer Alek Komar, suffering from a particularly deleterious cataract, had a $23k operation to replace the lens in one eye with a synthetic lens. One side-effect, apart from greater acuity of vision: he can now see into the ultraviolet.

If only it was that easy to get more high frequencies out of seismic data; the near-surface 'cataract' is not as easily excised.

This regular news feature is for information only. We aren't connected with any of these organizations, and don't necessarily endorse their products or services. 

Rotten writing's rubbish, right?

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Marked-up copy — effective copy editing is a useful skill for all scientists that writeI love teaching. I get a buzz from it. I don't know that I'm great at it, but I want to be great. As a student, I think I was quite reflective—both of my parents were teachers—and one of the great things about teaching is that you finally get to put your money where your mouth is. Every time you berated a teacher's boringness (behind their backs, obviously), or whined about how pointless an essay or lab exercise was (to your buddies), is now held up as a vivid and uncomfortable challenge. 

So late last year I got in touch with the Canadian Society of Petroleum Geologists (CSPG) and the US Society of Exploration Geophysicists (SEG) and offered a one-day short course. They both said they'd been wanting to offer something like it and, if enough people sign up for it, the course will run at least twice this year:

My worry is this: writing is like driving—most people think they're pretty good at it. But my course isn't just about style, it's also about tools, publishing, and getting things done. My two goals for the day are:

Get more people writing. Especially people from industry, who often excuse themselves from the global scientific community. 'I don't have the time' or 'My work's not interesting enough' are the things I hear. And maybe I'm a shallow, superficial kind of person, but I'm not so worried about high-brow, highly specialized, technical writing. There's plenty of that. I just want to see more grass-roots experience, stories, tutorials, field trip reports, how-to's, and what-I-did-at-the-weekend's. More community, in less traditional media.

Get people thinking about good style. Style has two aspects: the qualitative (what we might call interestingness) and the quantitative (correctness).  I don't claim to be the world's greatest writer myself, but I know what gets me good feedback in my work, and I have an eye for detail (did you notice the extra space back there? I did). I think there are two insidious notions out there about writing: science is serious business, and 'nit-picky' detail is not all that important. Both of these notions are nonsense.

If you were to take a writing skills course like this, what would you want to do or see? If you've done a course like this before and loved it (or not!), what can I learn from it? 

Apologies to Jon Agee for the title; his poem Rotten Writing, in his book Orangutan Tongs was the inspiration.