GP regression to interpolate/map Argo profile data. Follow the algorithm from Kuusela and Stein 2018.
Project 5: Local spatio-temporal interpolation of Argo data
Mentors: Alison Gray, Dhruv Balwada, Spencer Jones
Specific tasks
- Import Argo T or S data from a specific region
- Fit the data to a mean function via least squares or loess and subtract the result from the data
- Estimate autocovariance parameters for the resulting anomaly field via maximum likelihood estimation
- Use those parameters to estimate the anomaly field via "objective mapping" The problem Optimal space-time interpolation of scattered oceanographic data in python; follows on methods from Kuusela and Stein (2018). Can use existing package (george) to compute likelihood and mapping. Application example Could be focused on any fairly small region (~5-10-degree box) in the part of the global open ocean well-sampled by Argo.
Practical steps:
- Import Argo data from selected region of interest (lat/long/depth). -- We could skip this initially and just make a script that takes an input dataset consisting of (lat, lon, time, data), which would be more easily applicable to any given dataset. Use Argopy
- Compute mean (large-scale signal). -- This can be done simply using a least squares fit to data, with a given set of basis functions such as 2D polynomial in space and a seasonal cycle in time. Can potentially use Scipy to do this. - see note 1 below.
- Subtract mean at data points from data values to get residuals.
- Determine parameters of the covariance function that describes the residual field via maximum likelihood estimation (optimize hyperparameters via george package).
- Use Gaussian process regression with optimized covariance parameters to compute an estimate at a given set of points (lat, lon, time) (via george package). Add this to the estimate of the large-scale mean to get final estimate.
Additional resources:
- Tutorials from George: https://george.readthedocs.io/en/latest/tutorials/first/ ; https://george.readthedocs.io/en/latest/tutorials/hyper/
- George example for 2D interpolation :https://gist.github.com/shoyer/80aa06f5ad44aacd9187
- List of useful links to learn more :https://hackmd.io/@eHN2gDGTS7uR1j3KZ26AJQ/ry8VfkAVL
- Argo: https://argo.ucsd.edu/
Note 1: regarding fitting the data to the mean state (in notebook 1), we can use linear least squares: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.lsq_linear.html#scipy.optimize.lsq_linear which finds the values of x that minimizes Ax - b, where b = array of measured data points and A is a matrix that has columns corresponding to the basis functions we are fitting to, evaluated at the data locations. For our basis functions, we can use 2D polynomials in lat,lon, plus seasonal harmonics that vary in time. This follows what is described in the Park 2020 text I uploaded. I would suggest seasonal harmonics up to order 2.
A few other things I found when doing this in matlab:
- It is helpful to transform everything into a coordinate system centered on some center point in space/time.
- Time should be used with units of days.
- Once we solve for x, we find the mean at the data locations by evaluating Ax, where again A is a matrix of the basis functions evaluated at the data locations.