seascapes: access HyCOM oceanographic model data

With Dan...

For generating environmental products, and deriving anomolies, want to access oceanographic model data that has values at depth (not just surface) and doesn't suffer from cloud cover issues.

HyCOM

The best candidate so far is probably the Hybrid Coordinate Model (HyCOM]. See HyCOM Data Server:

HYCOM + NCODA Global 1/12° Analysis Date Range: 2008-09-19 to Present
HYCOM + NCODA Global 1/12° Reanalysis Date Range: 1992-10-02 to 2012-12-31
HYCOM + NCODA Gulf of Mexico 1/25° Analysis Date Range: 2003-01-01 to Present

For a great overview of the HyCOM data product and issues with extraction, projections, etc, see HYCOM – Marine Geospatial Ecology Tools:

HyCOM doesn't suffer from cloud cover and is available at multiple depths:
HyCOM has some funky projection aspects:

For more on slicing the netcdf files using OPeNDAP and constructing URLs for given indices, check out QuickStart - OPeNDAP Documentation.

MGET

The Marine Geospatial Ecology Tools (MGET) has a great set of tools specific to fetching HyCOM data if you want to use ArcGIS ModelBuilder to extract.

MGET HYCOM.py: Python code to access HyCOM data, but might depend on ArcGIS for generating climatologies

R

Ideally, we use something more easily scriptable within a common platform like R. For more on getting setup with R & RStudio, see MBON Help - Setup Software for Reproducible Research.

A great resource for finding out the latest recommended packages to use for a given task, is the CRAN Task Views. For instance, SpatioTemporal Task View suggests using ncdf4 (and pbdNCDF4 adds parallel processing cababilities). Also see ncdf4.helpers: a collection of helper functions for dealing with NetCDF files opened using ncdf4. If data type is compound, might try rancid.

Another great package is rerddap, a general purpose R client for ERDDAP servers (see rerddap introduction).

Here are a few tutorials:

netCDF in R | geog.uoregon.edu
rerddap - get gridded data in month chunks - Gists - rOpenSci Discuss using hycom_gom310S

R: obtain a specific depth from multi dimension array of depth levels - Stack Overflow

library(ncdf4)

file <- "http://ncss.hycom.org/thredds/ncss/GLBa0.08/latest/temp?var=temperature&north=25&west=74.1199&east=434.1199&south=-15&horizStride=1&time_start=2016-09-27T00%3A00%3A00Z&time_end=2016-09-27T23%3A59%3A00Z&timeStride=1&vertCoord=&accept=netcdf4"

savefile = tempfile(, fileext = "nc4")
download.file(file, savefile)
ncdata <- nc_open(savefile)
lon <- ncvar_get(ncdata, "Longitude")  
lat <- ncvar_get(ncdata, "Latitude") 
temp <-ncvar_get(ncdata,"temperature")

temp <- temp [,,1:10] # subset depths to speed up
depths <- 1:10  # let's define some dummy depths - you want to put actual values, here !

finddepth = function(pixtemp, ...) {
if (max(pixtemp, na.rm = TRUE) < predtemp$temp) {
  NA    # set to NA if no values >= 25
} else {
  depth <- tryCatch({
    depth <- approx(pixtemp, depths,predtemp$temp)$y # interpolate using linear (faster)
    # interp  <- loess(depths~pixtemp)  # interpolate using loess  (slower - deals with non-linearity)
    # depth  <- predict(interp, predtemp$temp) # find depth @ temperature
    return(depth)   # send back computed depth
  }, error = function(e) {NA}
  )

}
}
predtemp  <- data.frame(temp = 25)   # set desired isotherm
iso_depth <- apply(temp, c(1, 2), FUN = finddepth)

library(lattice)
levelplot(iso_depth, main = "Isotherm depth", col.regions = terrain.colors(250))

Accessing LOCA Downscaling Via OPeNDAP and the Geo Data Portal with R. - The USGS OWI blog

Matlab

Import NetCDF Files and OPeNDAP Data - MATLAB & Simulink

EDC Connector GUI

The Environmental Data Connector (EDC) is a tool that allows users to connect to THREDDS/OPeNDAP/SOS/ERDDAP servers and download environmental data.

It was developed for the National Oceanic and Atmospheric Administration (NOAA) Fisheries by RPS Applied Science Associates (ASA). Version 1.3.5 of the EDC is available in five versions: EDC for ArcGIS 10.X, EDC for Matlab, EDC for R, EDC for Excel and EDC Standalone.

EDC Product Downloads

marinebon / sdg14