Expedition Software

Preparing a Heard Island image taken with the NASA Aqua/MODIS instrument using GIMP.  Image credit: Bill Mitchell (CC-BY).
Preparing a Heard Island image taken with the NASA Aqua/MODIS instrument using GIMP. Image credit: Bill Mitchell (CC-BY).

Previously, I’ve written a little about the computer issues that may come up on the Heard Island expedition, as well as some of my views on open access (I’m generally for it). Now I’d like to talk a little bit more about the software which will be on the expedition computers.

For the most part, we’re using open-source software wherever it’s practical. My heart broke a little when I realized we would not be able to run Linux for many of the computers because of some of the programs needed to support the ham radio side of the expedition. I prefer open-source software because it can help encourage experimentation and learning among amateur programmers, it has code which is verifiable (not subject to security through obscurity), can be shared freely, and does a better job supporting open formats free of restrictive proprietary specifications that force vendor lock-in.

Here are some of the software packages which are coming with us:

  • GIMP (the GNU Image Manipulation Program), for raster graphics
  • Inkscape, for scalable vector graphics
  • Firefox, for standards-compliant HTML browsing
  • FileZilla, an FTP client for sharing files over the (local) network
  • PuTTY, a command-line client for accessing remote computers
  • VLC (VideoLAN Client), for playing sound/video files
  • Audacity, an audio recording/editing program
  • Pidgin, a chat client
  • LAMP (Linux, Apache, MySQL, PHP), a web server and related programs/languages (probably coming, but not confirmed)
  • QGIS, a mapping/geospatial information system

Just as with ecology, having a healthy, diverse software ecosystem is important. It allows new ideas a chance to thrive, and for users who know what they are doing to add features and patch bugs themselves. More and more academic research is turning toward open-source tools, from R (statistics) to Git (of GitHub fame) to WordPress. We are choosing as much open source software and as many open formats as possible to help preserve the data for the future. Proprietary formats are subject to the corporation changing the format to force upgrades, vendors going out of business, and other issues. It also happens with open-source projects, but there are generally compatible programs which can handle your data.

Most of these programs above are ones I have been using for quite a while, and have significant user bases. Online support is pretty easily accessed via search engine. Try them out at home, and you may find them quite to your liking!

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Expedition Planning

Expedition route from Cape Town to Heard Island to Fremantle.  Image credit: Bob Schmeider/Cordell Expeditions.
Expedition route from Cape Town to Heard Island to Fremantle. Image credit: Bob Schmeider/Cordell Expeditions.

This past weekend, I was in California meeting with people involved in the Heard Island expedition. Just five months from now, the ship is expected to arrive at the island after ten or eleven days at sea. With departure so soon at hand, preparations are in full swing, and boxes are being assembled for shipping to South Africa.

This weekend we discussed the protocol for preparing computers to come on the expedition. Usually, most people think little about computers connecting to a network: either it has a connection or it doesn’t. If there’s a connection, we typically have a relatively high data bandwidth and pages load quickly.

However, on Heard Island, although we will have satellite communications to keep us connected, the data bandwidth will not be especially high. More to the point, when data costs $7/MB, economizing bandwidth is essential. Sure, we can choose not to load webpages with lots of images, or watch videos on YouTube, but there’s another issue: automatic updates.

Many computer programs (e.g. Windows, web browsers, anti-virus, etc.) like to automatically download and install updates. Some of these can be quite large. It is essential, therefore, that immediately prior to the expedition, all updates be turned off (and a list made of which were turned off, so they can be turned on again upon our return to the networked world). The only network traffic which should go over the satellite link should be traffic which we explicitly allow, that which is needed for the successful completion of the expedition. Yes, we might check email occasionally, or write a blog post or tweet, but we will do that sparingly. Automatic updates will not be so conscientious, and will incur significant costs.

Already we are going through the software installed on the computers—both expedition computers and personal computers—and making a list of programs which automatically phone home and check for updates. Those will need to be disabled before the expedition leaves port.

Geoscientist’s Toolkit: Terra MODIS

Terra satellite being prepared for placement in the payload fairing.  Image credit: NASA (public domain).
Terra satellite being prepared for placement in the payload fairing. Image credit: NASA (public domain).

In my previous post on satellite communications, I discussed two types of satellites: geostationary and low-Earth-orbit. One of NASA’s low-Earth-orbit satellites, orbiting at an altitude of 705 km (438 mi), is Terra.

Launched in December of 1999, Terra is in a polar orbit, and is sun-synchronous—it makes its north-to-south pass on the daylight side of Earth, crossing the equator around 10:30 AM in the local time zone. As 10:30 AM moves around the Earth, so too does Terra, with each orbit taking 99 minutes.

Aboard Terra is one of my favorite instruments: the MODerate resolution Imaging Spectroradiometer, or MODIS. Unpacking the name, we find that MODIS has moderate resolution: its best resolution is about 250 m/pixel. It is an imaging instrument (i.e. it sends back pretty pictures), and it is a spectroradiometer, meaning that it measures the amount of light (radiometer) across a spectrum of wavelengths (visible and infrared, in this case). Most of my use of the instrument is for its true-color imagery, or “Bands 1-4-3” (corresponding to red, green and blue). An example image is shown below.

Minneapolis area seen by NASA's Terra satellite Sept. 30, 2015.  The Minneapolis and St. Paul airport is the concrete-colored smudge just left of center; St. Cloud is in the upper left, Winona toward the bottom right, and at furthest bottom right is La Crosse, WI.  Image credit: NASA (public domain).
Minneapolis area seen by NASA’s Terra satellite Sept. 30, 2015. The Minneapolis and St. Paul airport is the concrete-colored smudge just left of center; St. Cloud is in the upper left, Winona toward the bottom right, and at furthest bottom right is La Crosse, WI. Image credit: excerpt from NASA imagery (public domain).

MODIS is a push-broom type imager. It takes one very wide “picture” (2,330 km East-West), and splits that into 36 spectral bands. As the spacecraft flies (North-to-South), those wide “pictures” are put together along the track of the satellite to create a swath image. The instrument’s resolution is highest at the center of the image.

One great thing about MODIS is that it has pretty good spatial coverage (that’s the advantage of the moderate resolution). In 24 hours, it will get images of most of the Earth, but with a few gaps between swaths at the equator. Orbits are offset day-to-day (with a 16-day cycle), so it takes two days to get full global coverage. Global maps are produced daily (give or take) by NASA Earth Observations, and tend to have a day or two of lag behind real-time.

Terra MODIS image of Earth, Oct. 7, 2015.  The tan-grey streaks in the center of the swath over some equatorial regions is caused by glare from the sun reflecting off the ocean surface.  Image credit: NASA Earth Observations (public domain).
Terra MODIS image of Earth, Oct. 7, 2015. The tan-grey streaks in the center of the swath over some equatorial regions is caused by glare from the sun reflecting off the ocean surface. Image credit: NASA Earth Observations (public domain).

You may notice that in the picture of the whole world, Antarctica is nicely lit up, but the data for the North pole is missing? What’s up with that? Is NASA taking part in a conspiracy with Santa to hide his gift-production and distribution facilities?

In a word: no.

In more words, having recently passed the September equinox (autumnal equinox to folks in the northern hemisphere), the North pole is now in darkness at 10:30 AM “local time”. It doesn’t really matter what you choose as local time, because it’s dark regardless. With it being dark, the instrument is off.

Beyond pretty pictures, Terra MODIS is used for scientific purposes. Its images can detect wildfires,[1] be used to estimate area burned by fires, monitor drought severity and snow cover, study aerosols and atmospheric pollutants, and even chlorophyll (phytoplankton) concentrations in the ocean.

Using the images to understand the productivity of plants can in turn influence the estimates for how much carbon is being removed from the atmosphere, and can serve as a gauge of ecosystem health in remote areas. Volcanic eruptions, major wildfire events, and even thick pollution from human sources can be seen in these images. By analyzing MODIS data, scientists can gauge how much of various types of atmospheric gases are being emitted by wildfires.[2, 3]

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[1] Near-real-time swath data are available from the Rapid Response website.

[2] Mebust, A. K., Russell, A. R., Hudman, R. C., Valin, L. C., and Cohen, R. C.: Characterization of wildfire NOx emissions using MODIS fire radiative power and OMI tropospheric NO2 columns, Atmos. Chem. Phys., 11, 5839-5851, doi:10.5194/acp-11-5839-2011, 2011. [Open access]

[3] Mebust, A. K. and Cohen, R. C.: Space-based observations of fire NOx emission coefficients: a global biome-scale comparison, Atmos. Chem. Phys., 14, 2509-2524, doi:10.5194/acp-14-2509-2014, 2014. [Open access]