Cut the small print

We received a contract for a new piece of work recently. This wouldn't normally be worth remarking on, but this contract was special. It was different. It was 52 pages long.

It was so comically long that the contracts analyst at the company that sent it to me actually called me up before sending it to say, "The contract is comically long. It's just standard procedure. Sorry." Because it's so long, it's effectively all small print — if there's anything important in there, I'm unlikely to see it. The document bullies me into submission. I give in.

Unfortunately, this is a familiar story. Some (mostly non-lawyers) like Alan Siegel are trying to change it:

Before we all laugh derisively at lawyers, wait a second. Are you sure that everyone reads every word in your reports and emails? Do they look at every slide in your presentations? Do they listen to every word in your talks? 

If you suspect they don't, ask yourself why not. And then cut. Cut until all that's left is what matters. If there's other important stuff — exceptions, examples, footnotes, small print, legal jargon — move it somewhere and give people a link.

When to use vectors not rasters

In yesterday's post, I looked at advantages and disadvantages of various image formats. Some chat ensued in the comments and on Twitter about making drawings and figures and such. I realized I hadn't been very clear: when I say 'image', I really mean 'raster' or 'bitmap'. That is, a discretized (pixel-based) grid of data.

What are vector graphics?

Click to enlarge — see a simulation of the difference between vector and raster art.What I was not writing about was drawings and graphics combining text, lines, and images. Such files usually contain vector graphics. Vector graphics do not contain descriptions of pixels, but instead they contain descriptions and positions of text, paths, and polygons. Example file formats are:

• SVG — Scalable Vector Graphics, an open format and web standard
• AI — a proprietary format used by Adobe Illustrator
• CDR — CorelDRAW's proprietary format
• PPT — pictures in Microsoft PowerPoint are vector format
• SHP — shapefiles are a (mostly) generic vector format for GIS

One of the most important properties of vector graphics is that you can rescale it without worrying about changing the resolution — as in the example (right).

What are composite formats?

Vector and raster graphics can be combined in all sorts of ways, and vector files can contain raster images. They can therefore be used for very large displays like posters. But vector files are subject to interpretation by different software, may be proprietary, and have complex features like guides and layers that you may not want to expose to someone else. So when you publish or share your work it's often a good idea to export to either a high-res PNG, or a composite page description format:

• PDF — Portable Document Format, the closest thing to an open, ubiquitous format; stable and predictable.
• EPS — Encapsulated PostScript; the precursor to PDF, it's rarely called for today, unless PDF is giving you problems.
• PS — PostScript is a programming and page description language underlying EPS and PDF; avoid it.
• CGM — Computer Graphics Metafiles are best left alone. If you are stuck with them, complain loudly.

What software do I need?

Any time you want to add text, or annotation, or anything else to a raster, or you wish to create a drawing from scratch, vector formats are the way to go. There are several tools for creating such graphics:

• Adobe Illustrator — the top banana, but pricey
• Inkscape — free and open source (our favourite)
• ACD Canvas
• CorelDRAW

Judging by figures I see submitted to journals, some people use Microsoft PowerPoint for creating vector graphics. For a simple figure, this may be fine, but for anything complex — curved or wavy lines, complicated filled objects, image effects, pattern fills — it is hard work. And the drawing tools listed above have some great advantages over PowerPoint — layers, tracing, guides, proper typography, and a hundred other things.

Plus, and perhaps I'm just being a snob here, figures created in PowerPoint make it look like you just don't care. Do yourself a favour: take half a day to teach yourself to use Inkscape, and make beautiful figures for the rest of your career.

Update on Friday, September 14, 2012 at 10:57 AM by Matt Hall

I just came across another nasty metafile format: Windows Metafile, and its dimwit sidekick, the Enhanced Windows Metafile. Watch out for wmf and emf file extensions. If your software spits them out at you, ask the developers if they wouldn't mind switching to something else — PDF or SVG would be nice.

How to choose an image format

Choosing a file format for scientific images can be tricky. It seems simple enough on the outside, but the details turn out to be full of nuance and gotchas. Plenty of papers and presentations are spoiled by low quality images. Don't let yours be one! Get to know your image editor (I recommend GIMP), and your formats.

What determines quality?

The factors determining the quality of an image are:

• The number of pixels in the image (aim for 1 million)
• The size of the image (large images need more pixels)
• If the image is compressed, e.g. a JPG, the fidelity of the compression (use 90% or more)
• If the image is indexed, e.g. a GIF, the number of colours available (the bit-depth)

Beware: what really matters is the lowest-quality version of the image file over its entire history. In other words, it doesn't matter if you have a 1200 × 800 TIF today, if this same file was previously saved as a 600 × 400 GIF with 16 colours. You will never get the lost pixels or bit-depth back, though you can try to mitigate the quality loss with filters and careful editing. This seems obvious, but I have seen it catch people out.

JPG is only for photographs

Click on the image to see some artifacts.The problem with JPG is that the lossy compression can bite you, even if you're careful. What is lossy compression? The JPEG algorithm makes files much smaller by throwing some of the data away. It 'decides' which data to discard based on the smoothness of the image in the wavenumber domain, in which the algorithm looks for a property called sparseness. Once discarded, the data cannot be recovered. In discontinuous data — images with lots of variance or hard edges — you might see artifacts (e.g. see How to cheat at spot the difference). Bottom line: only use JPG for photographs with lots of pixels.

Formats in a nutshell

Rather than list advantages and disadvantages exhaustively, I've tried to summarize everything you need to know in the table below. There are lots of other formats, but you can do almost anything with the ones I've listed... except BMP, which you should just avoid completely. A couple of footnotes: PGM is strictly for geeks only; GIF is alone in supporting animation (animations are easy to make in GIMP). 

All this advice could have been much shorter: use PNG for everything. Unless file size is your main concern, or you need special features like animation or georeferencing, you really can't go wrong.

There's a version of this post on SubSurfWiki. Feel free to edit it!

Update on Wednesday, August 8, 2012 at 12:24 PM by Matt Hall

Don't miss the following post, When to use vectors not rasters, all about vector and composite formats. Together, these posts should get you started with creating great scientific graphics. Let us know how you get on!

The evolution of open mobile geocomputing

A few weeks ago I attended the EAGE conference in Copenhagen (read my reports on Day 2 and Day 3). I presented a paper at the open source geoscience workshop on the last day, and wanted to share it here. I finally got around to recording it:

As at the PTTC Open Source workshop last year (Day 1, Day 2, and my presentation), I focused on mobile geocomputing — geoscience computing on mobile devices like phones and tablets. The main update to the talk was a segment on our new open source web application, Modelr. We haven't written about this project before, and I'd be the first to admit it's rather half-baked, but I wanted to plant the kernel of awareness now. We'll write more on it in the near future, but briefly: Modelr is a small web app that takes rock properties and model parameters, and generates synthetic seismic data images. We hope to use it to add functionality to our mobile apps, much as we already use Google's chart images. Stay tuned!

If you're interested in seeing what's out there for geoscience, don't miss our list of mobile geoscience apps on SubSurfWiki! Do add any others you know of.

Well worth showing off

Have you ever had difficulty displaying a well log in a presentation? Now, instead of cycling through slides, you can fluidly move across a digital, zoomable canvas using Prezi. I think it could be a powerful visual tool and presentation aid for geoscientists. Prezi allows users to to construct intuitive, animated visualizations, using size to denote emphasis or scale, and proximity to convey relevance. You navigate through the content simply by moving the field of view and zooming in and out through scale space. In geoscience, scale isn't just a concept for presentation design, it is a fundamental property that can now be properly tied-in and shown in a dynamic way.

I built this example to illustrate how geoscience images, spread across several orders of magnitude, can be traversed seamlessly for a better presentation. In a matter of seconds, one can navigate a complete petrophysical analysis, a raw FMI log, a segment of core, and thin section microscopy embedded at its true location. Explore heterogeniety and interpret geology with scale in context. How could you use a tool like this in your work?

Clicking on the play button will steer the viewer step by step through a predefined set of animations, but you can break off and roam around freely at any time (click and drag with your mouse, try it!). Prezi could be very handy for workshops, working meetings, or any place where it is appropriate to be transparent and thorough in your visualizations.

You can also try roaming Prezi by clicking on the image of this cheatsheet. Let us know what you think!

Thanks to Burns Cheadle for Prezi enthusiasm, and to Neil Watson for sharing the petrophysical analysis he built from public data in Alberta.