pf_geolocation

Particle filter geolocation in Python for Data Storage Tags

Dependencies

This code requires the following packages:

• Basemap (pyproj)
• filterpy
• netcdf4
• pytides

For the GPU version the following are required in addition:

• CUDA (see NVIDIA CUDA official documentation for instructions)
• PyCUDA

Preprocessing

Either of the following may be used to preprocess raw data from DSTs manufactured by Star-Oddi or Lotek:

• The preprocessing code for hmm_smast, available at https://github.com/cliu3/hmm_smast/tree/dev/test/preprocessing;
• An R code package; available at https://github.com/cliu3/R_HMM_Preprocessing.

Publications

Liu, C., Cowles, G.W., Zemeckis, D.R., Fay, G., Le Bris, A., Cadrin, S.X. (2019), A hardware-accelerated particle filter for the geolocation of demersal fish. Fisheries Research, 213C(2019):160-171. doi:10.1016/j.fishres.2019.01.019.