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

The reverberations from TRANSFORM 2021 have started to dampen, so we’re back with our weekly round-ups.

Badges of honour — Did you know that you can slap a Software Underground badge on your projects and webpages? These badges aren’t just for showing off either. They can links to other places, for instance to your project’s channel in the Swung Slack, if it has one.

Geothermal Hackathon 2021 — is taking place at the end of next week with much activity to be going on in the #geothermal-hack-2021 channel. Here are some of the proposed projects. Even if you aren’t registered in the hackathon you can still follow the action.

Superstar with LiDAR — Are you dealing with .las files, but not of the wireline kind? Then this discussion will serve you up a platter of resources and advice for working with point-cloud data sets.

Feature combo pipelines — If, like Brendon, you’re doing some machine learning and you find yourself building a boatload of models all with different combinations of inputs and pre-processing steps, you’re life is going to be much easier if you have a way to keep track of these different permutations so you can apply it all again on other data.

Need a license for work — Pythonistas using Anaconda might be shocked to find out that it’s no longer free to use. Sort of. It depends on who you work for and the kind of work you are doing. This thread discusses the issues and reveals a shared frustration in comprehending the terms and conditions. There are also some thoughtful perspectives on supporting the free (or nearly free) software that many organizations become increasingly dependant on.

Tools for seeing — Geoscience very often relies on making graphics and visualization. This post pointing to the Python-only compilation called PyViz.org, shows you the collection of tools that are out there. It looks to be a comprehensive resource, particularly because the number of tools in the tool shed can seem so daunting.

News from the Underground

Here’s what happened in the Underground this last week in February.

Rendezvous numéro trois – Matteo Ravasi’s Rendezvous was on Friday, but don’t worry, you can catch what you missed on YouTube. He showed off some of the amazing things in PyLops and in a talk entitled, Solving geophysical inverse problems on GPUs with PyLops+cupy. If you’re into signal processing, inverse problems, and data reconstruction, you need to check it out..

Conflicts to declare – Kieran’s shared his frustration about a semi-anonymous reviewer on a manuscipt complaining that the open-source tool that was the topic of the paper was not novel, because closed-source commercial software exists that does the same thing. The discussion that follows has some interesting opinions on bias, conflict of interest, and fishing for the science in the murky waters where commercial software lurks.

Seismic unrest in Iceland – The geology hosting those gorgeous pictures of the Blue Lagoon in your Instagram feed, could soon see a once-in-a-millennium eruption, based on its current unrest and its historical record. A swarm of earthquakes are happening on the Reykjanes Peninsula.

A license to work together – What do you get when a software vendor wants to contribute to some open source software… but doesn’t like the licence? Discussion here. One quote:

“Digging in over BSD-3 vs Apache 2 seems like refusing to volunteer at your local soup kitchen because they serve Hunt’s ketchup not Heinz.”

News from the Underground

Here are some highlights from the Software Underground Slack this week.

Increasing dtype diversity — Progress is being made within NumPy to handle more diverse datatypes which would allow for ndarrays to carry information about units and other things. There’s been lots of other chat in the #python channel this week; check it out.

Micro-editors wanted — The collaborative book project, 52 Things You Should Know About Geocomputing has amassed the requisite number of articles and is undergoing review. And what better way to edit a collection of essays than with a collection of editors? The articles are less than 800 words and cover a very wide range of topics. So if you’re interested in helping with the review, pop into the #52things channel and say hello.

Quantitative blobology? — One question this week spurred a lot of discussion about how to do more quantitative things with amplitude maps. The thread brings up uncertainty, subjectivity, and information theory. Threads like this are always a goldmine of insight and information, check it out.

Choosing open licences — A discussion on open licences for content, code and data brought out some useful links, and led to Matt writing a blog post about choosing licences for open science.

Digital rocks — One of the great challenges of subsurface science and engineering is that we usually cannot directly measure the thing we are interested in. Interested in lithology down a borehole? You can count gamma rays. Want to know the amount of pore space? Scatter some neutrons or bounce some sonic pulses around. Check out this thread discussing synthetic forward modeling and inversion of petrophysical data, and pointing at GebPy (pictured here), an interesting new tool for petrophysics.

GebPy, as pictured in Maximillian Beeskow’s Twitter post.

That’s it for this week, what did I miss?