News from the Underground

In the seemingly random content factory that is the Software Underground community, there has been a heavy sampling this past week around openness. What is open source? What is open data? What are good practices? and, How does this affect me? Here’s a collection of those conversations and more.

The Geothermal Hackathon — happened last week immediately following the World Geothermal Congress Geoscience virtual event. You can read about the things that people built leveraging open data sets and be sure to connect with these creators in the #geothermal channel.

The complicated world of open source — Spilling over from an SPE workshop on Open Software, is perhaps the longest thread in Swung history about what actually constitutes open source software, why it can be so confusing, and what the implications are for scientists and technologists. Matt followed up with a number of suggestions how technical societies can support openness, and also created a poll to measure the degree of confusion around open source. Conclusion: it depends.

A checklist for open scientific software — Yes, open source is complicated, especially for newcomers, so it seems fit for relatively straightforward tools to guide behaviours. Matt shared a so-called best-practice checklist for open scientific software, which quickly underwent a handful of revisions after some supportive feedback. It is meant to be more than just tick marks on a piece of paper but that it can be a vehicle for delivering behavioural change.

Big Borehole Dig – Steph shared a cool project launched by the British Geologic survey welcoming scientists and citizen scientists alike to digitize their vast collection of historic logs into a standard digital format. It’s the ‘ol PDF to actually-digital transformation challenge and this one is a tall order. But just imagine the data science possibilities from 1.4 M boreholes!

Tools and tactics – people are getting help on to tricky technical questions in the #python channel on a variety of topics including: dealing with very large tabular data with Vaex, how to constrain solutions to non-linear problems with scipy.optimize, and fixing missing data values in rasters with rasterio.

Vedo – in the visualization awesomness category, the winner goes to a post that Dieter made in the #viz channel about the Vedo project, whose gallery will incite all the feels of a kid in candy store for those working in 3D. Notably, the first tile in the gallery is a demo geo-model shared by Richard Scott. Check out his scene here before you get on with the rest of your day.

Vedo – a python module for scientific analysis and visualization of 3D objects.

News from the Underground

Here’s all the news from the Underground this week…

Have you signed up for TRANSFORM 2021 yet? Because it kicks off with the hackathon next Friday 16 April. The hackathon projects are starting to take shape and there is going to be a special Rendezvous session on next Wednesday 14 April at 16.00 UTC to discuss project ideas. Come along and let the project ideas wash over you and vie for your attention.

What to learn first? — Matt created an infographic entitled, Which language should I learn first? with some opinions about how to get started in programming for science, business, and fun. There’s more context in his blog post and this thread contains some good perspectives from others. There’s quite a bit of chat on Twitter about it too.

Colour science for colouring science — Alessandro’s posted in the #viz channel an excerpt from one of Edward Tufte’s books, appealing to those particular colour orderings that “have a natural visual hierarchy”. Check out the thread for some thoughtful considerations concerning the state of the art for colouring data.

Image modified from fabriocrameri.ch.

Singing with the birds — Jesse shared an article in #random with the opening line, “I had a dream one night where a blackbird was talking in human language”. The article then ventures into an exploration of converting human speech into birdsong. If you’re into signal processing, acoustics, and ornithology, you’re going to think this is really cool.

As always, if you want to highlight anything in these weekly posts, message @Evan on Swung.

News from the Underground

Things were pinging away in the main channels this week, with a few posts garnering loads of enthusiasm and important chatter.

The weirder the better — In the #viz channel, Nathan announced the latest Xeek challenge, Keep Geoscience Weird. This competition is all about new and novel ways of visualizing subsurface data. It’s a very open-ended competition — you can use any data that you like, as long as it’s related to the subsurface. I highly recommend reading the thread concerning the Terms & Conditions and motivations for engagement.

Sand vs shale — The longest thread of the week (150+ messages!) was in the #sedimentology channel. A simple question about computing running averages led to uncovering a bug in striplog, some plots (right), a hackathon project, and some weirdness in how Microsoft Excel exports CSV files.

Hello OSDU, how do you do? — The Open Subsurface Data Universe (OSDU) Forum is a consortium of ~200 members and is rolling out the first production release of its platform this week. For a bit of history on how the OSDU came to be, who’s involved, and where it’s headed, this thread might be a good summary.

But seriously. Who’s with me? — Has anyone ever given any serious consideration to prospecting and mining asteroids or other planetary bodies for resources? Turns out they have.

Teeny weeny ancient plant bits — Kieran threw some Carboniferous kerogen samples into the SEM and shared these gorgeous images. The discussion drifted naturally to “should I put 300 of these images online somewhere for others to look at and play with?”

How to get lost — Kleo asked for recommendations for introductory Python exercises, and got a load of responses. A few folks pointed to last year’s TRANSFORM tutorials. In another channel, Heba got a somewhat philosophical perspective from Hallgrim on the pursuit of programming: “[it’s] all about getting lost, banging your head against the wall, and the extreme pleasure of breaking through the wall. You are already lost, you’ve already found this community, so you have a great talent for what is ahead of you…”.

What was your favourite thread of the week?

News from the Underground

What’s new? Here are the highlights from the last seven days.

Strikes and dips and tadpoles — What tools would you recommend for working with structural data in boreholes? Lots to choose from, among them fractoolbox — as well as the wireline log and standard image processing libraries.

Geovisual — Speaking of interesting plots, some new visualization libraries came under the spotlight: one a d3.js library for ternary plots, and the other discussing pyrolite, a Python library for doing all sorts of geochemistry-related plots.

All the colours – Seismic interpreters have likely heard of spectral decomposition – the partitioning of seismic into three frequency bands that you can plot as RGB blended images. This work in progress uses a bag of different tools, some of which might get stitched closer together given the right motivation and use cases.

Thermal under-where? The World Geothermal Congress has been virtualized and spread out across several weeks, and the Swung-powered Geothermal Hackathon is starting to take shape. Chime in now to influence the agenda and help shape the happenings.

NetCDF to ipygany — I wrote about ipygany a couple of weeks ago, and here Wes is showing off how to take your NetCDFs and drop them right into the notebook environment.

No mouse clicks allowed — Lastly, In a heartwarming testament to the nature of our connection to science and software, John Armitage tells a short tale about the time he met a little library called GemPy and how it helped him build an earth model entirely out of code. No mouse clicks allowed! Sadly, external forces intervened and John had to build his model all over again using proprietary point-and-click software which worked of course… until it didn’t.

Stories like this remind us why reproducible science is the best science. If you have tales of open science glory — or woe! — consider sharing them in the Software Underground.

News from the Underground

Another week, another batch of highlights from the world of Software Underground.

Before we get to the nuggets from Slack, there have been a few changes to the website. The front page is new, and there’s a new page explaining why Slack is so cool, in the hope that more people sign up and take part in those conversations. There’s also a new page for potential sponsors, and you can now register for TRANSFORM virtual conference — or buy a T-shirt!

You don’t have to wait for TRANSFORM to hear about subsurface geophysics. There are two Subsurface Rendezvous events coming up in February — from Sean Walker and Matteo Ravasi — read all about them on the website. Both promise to be unmissable… and they’re free!

As usual, the Slack chat has also been active; here are some highlights:

Entwine – A posting about a USGS service for viewing and analyzing lidar datasets in your browser caught my attention. It’s always fun when you can click on a link and immediately start playing around.

Look at all those buttons!

Plan for redundancy. There was a post about the Women in Geothermal (WING) organization this last week. Their vision is short and brilliant and worth repeating: “The aim is to one day become redundant, where no group needs to advocate for gender equality.”

Can you see my faults? Elwyn Galloway posted about a Voila app that makes a forward model of a normal fault. Go and slide the sliders. Apps like this are fun to see — interactive, single purpose, on the web, shareable. And built entirely using open source code, with attribution.

Yet another visualization library for Jupyter? Yes! If you’re looking to make interactive 3D visualizations in Python you’ve got load of tools to choose from: PyVista, IPywidgets, Bokeh, IPyVolume, and more (info and links at PyViz.org). There’s new one to check out called ipygany with all sorts of cool features made awesomer by using your GPU.

As usual, if I missed something cool, let us know in the comments. And if you spot anything hot in the coming week, drop tips in the comments or in Slack.