Processing code for MODIS sea surface temperatures to estimate surface and subsurface ocean temperatures near Sermilik Fjord
The included polar.nix derivation will build an environment to execute the iPython notebook and dependencies. If you already have nix, just run "nix-shell polar.nix" from the directory with polar.nix.
If you don't have nix in your path, installation instructions are here*:
https://nixos.org/download.html
*because we can't have nice things, MacOS (Catalina) restricted all access to the root directory, so nix can't install to /nix. You can create an APFS volume that mounts at /nix. See instructions here:
https://dev.to/louy2/installing-nix-on-macos-catalina-2acb
There are two libraries that need to be installed manually by pip from within the nix-shell. The first is pyhdf, which is needed to open the MODIS files; it can be installed with:
pip install git+https://github.com/espg/pyhdf.git
The other library is pyorbital, which can similarly be installed with:
pip install git+https://github.com/espg/pyorbital.git
Note that both of these libraries are forked from the mainline repos and modified to work (pyhdf has a naming convention problem with the build libraries, and pyorbital is feature behind in terms of being able to parse TLE archives).
Please cite the paper below if you use this code and we highly recommend contacting the author (tasha.snow@colorado.edu) before using the code to ensure its reasonable application.
The MODISsstExtraction file samples MODIS SSTs from the MODIS 4 km products and produces a daily time series for each sampling region (Irminger Current, East Greenland Coastal Current, and the "Shelf Trough" along the bathymetric trough leading to Sermilik Fjord).
The MOD29 file creates the sea ice masks for the SSTs, which is used in the Extraction file.
MODIStimeseries file uses the extracted MODIS SSTs and processes them as described in:
Snow, T., Straneo, F., Holte, J., Grigsby, S., Abdalati, W., & Scambos, T.(accepted). More than skin deep: sea surface temperature as a means of inferring Atlantic Water variability on the southeast Greenland continental shelf near Helheim Glacier. Journal of Geophysical Research: Oceans. doi: https://www.essoar.org/doi/abs/10.1002/essoar.10503490.1