Extracting NOAA sea surface temperatures with ncdf4

I’ve written previously about some example R scripts I created to extract sea surface temperature data from NOAA’s Optimum Interpolated Sea Surface Temperature products. If you want daily global sea surface temperatures on a 0.25×0.25° grid, they gather those into 1-year files available at http://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.highres.html. If you want weekly average SST values on a 1×1° grid, you can get those back to 1981 at http://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.html. If you just want a smaller file for a single day on the 0.25×0.25° grid, you can find those at http://www.ncdc.noaa.gov/sst/griddata.php.

Continue Reading

Revised Open Wave Height Logger battery tests

The Open Wave Height Logger is meant to be a submersible pressure logger that will record absolute pressure at 4Hz for several months to give a record of wave height, and ideally do this on a single set of 3 D-cell batteries. I have recently made a few changes to the OWHL software, and discovered a major flaw in my original battery test. As a result, I have begun a new round of battery tests. The hardware and software changes are described here, and new battery test results are shown at the bottom of the page.

I was … Continue Reading

The effect of water temperature on whelk drilling speed

Last year I published a little paper showing how whelks (Nucella lapillus) drill through mussel shells at different rates depending on water temperature. This involved making hundreds of hours of recordings of whelks slowly scraping their way through the calcium carbonate shell of Mytilus edulis mussels in different water temperatures. The video above includes two examples of those recordings from two different snails of the same size, highlighted as red dots on the graph in the video, one taken at a water temperature of 9°C (48°F) and the second at 17.5°C (63.5°F). What you’ll notice … Continue Reading

ffmpeg time lapse notes

ffmpeg is a movie-encoding command line tool that is also useful for capturing and assembling time lapse movies, particularly using webcams. Below are some example commands to get it to do stuff. It is run from a terminal command line on Linux, OSX, and Windows. You will probably want to add the location of the ffmpeg files to your system PATH so that you can invoke ffmpeg from any directory.

The code shown here is specific to Windows 7 and later machines, so some commands will not work on OSX or Linux. Specifically, Windows uses the “dshow” option for … Continue Reading

Early Open Wave Height Logger battery tests

The Open Wave Height Logger prototype stack.

The Open Wave Height Logger prototype stack.

Following on the previous post about the Open Wave Height Logger project, I’ve been conducting a simple battery life test. One of the prototype OWHLs was powered by a 3 D-cell alkaline battery pack and shoved in the freezer for 32 days. The image below shows the collated daily data files for that time period, during which the data logger was sampling 4 times per second continuously. The black line is pressure in millibar, … Continue Reading

Open Wave Height Logger

OWHL – The Open Wave Height Logger
OWHL is a project originally dreamed up by Jarrett Byrnes and Ted Lyman at UMass Boston. Early on they contacted me for my thoughts on how to accomplish the goal of making a cheap, long-life pressure sensor data logger that could be used to record ocean wave heights near shore. I joined the effort during the initial specification stages. Ideally this device could be mounted on the seafloor at ~10 meters depth offshore, and record surface waves at 4 Hz for many months, with data saved to a micro SD card in a … Continue Reading

Lizards

Smug looking lizards.

Papoose_narrows_lizard_13

Midday, 100mm f/8

Papoose_narrows_lizard_16

100mm f/8

They seem awfully contented.

Thomson Reuters Web of Science is still using OCR text recognition for new citations?

A co-author emailed me the other day to point out that somehow my name had been misspelled in the Web of Science citation database on our recent paper in Ecological Applications.

The Web of Science listing has my first name listed as “Luice”, which judging by the name of this here website, isn’t how you spell my first name. Thomson Reuters managed to replace the “k” in my name with an “ic”. That looks suspiciously like an optical character recognition (OCR) error , which you might have run into if you’ve ever scanned in an old document and … Continue Reading

Arduino code for MS5803 pressure sensors

I have recently been developing a library for the Measurement Specialties MS5803 line of digital pressure sensors. These sensors are available in several different pressure ranges from 1 to 30 bar, they are submersible if installed in a proper housing, they communicate via I2C or SPI, and they cost around US$35. It’s fairly straightforward to interface the MS5803 with a microcontroller like the Arduino that can also communicate via the I2C or SPI protocols. They are a surface-mount style chip, meant to solder onto a 1.27mm pitch SOIC-8 layout (like the green board I used in the picture below). … Continue Reading

NOAA OISST v2 High Resolution daily sea surface temperatures with R

Update, 2015-11-30 It appears that NOAA has gone through and upgraded all of the OISST files to the newer version of the NetCDF file format. As a result, the functions outlined in this post don’t work any longer. Instead, see the updated functions in my newer post, http://lukemiller.org/index.php/2014/11/extracting-noaa-sea-surface-temperatures-with-ncdf4/. The concepts are the same as described here, but the newer functions use the ncdf4 package to access the newer NetCDF file format.

The National Ocean and Atmospheric Administration generates freely-available world-wide estimates of mean daily sea surface temperature, and has been doing so back to 1981. The data are on … Continue Reading

Page 4 of 11« First...23456...10...Last »