Source code for salishsea_tools.UBC_subdomain

# Python script for extracting a subset of Live Ocean results
# ---------------------------------------------------------------------------
# Usage
# From command line:
# python filename1 filename2 filename3 ...
# Inside python:
# import UBC_subdomain
# UBC_subdomain.get_UBC_subdomain([filename1, filename2, filename3,...])
# ----------------------------------------------------------------------------
# Description
# Creates new netCDF files that store a subdomain and subset of variables
# for UBC users (S. Allen's group).
# New file names are derived from the original file name with '_UBC' suffix.
# For example: becomes
# ----------------------------------------------------------------------------
# Written by
# Nancy Soontiens 2016

import sys
import netCDF4 as nc

# Bounds of subdomain (rho grid)
XBS = [55, 80]  # x-limits
YBS = [295, 325]  # y-limits
# Variables to copy
VAR_LIST = ['salt', 'temp', 'h', 'lon_rho', 'lat_rho', 'mask_rho', 'pn', 'pm',
            's_rho', 'hc', 'Cs_r', 'Vtransform', 'zeta', 'ocean_time',
            'lon_u', 'lat_u', 'mask_u', 'u',
            'lon_v', 'lat_v', 'mask_v', 'v',
            'NO3', 'phytoplankton', 'zooplankton', 'detritus', 'Ldetritus',
            'oxygen', 'TIC', 'alkalinity', 'CaCO3', 'rho']
# Dimensions to copy
DIM_LIST = ['xi_rho', 'eta_rho', 'N', 's_rho', 'ocean_time',
            'xi_u', 'eta_u', 'xi_v', 'eta_v']

[docs]def get_UBC_subdomain(f_list): """Create subdomain files for all netCDF files in f_list """ for fname in f_list: fnew = '{}'.format(fname.split('.nc', 1)[0]) with nc.Dataset(fname) as G, nc.Dataset(fnew, 'w') as Gnew: _copy_netCDF_subdomain(G, Gnew, XBS, YBS, VAR_LIST, DIM_LIST)
def _copy_netCDF_subdomain(oldfile, newfile, xbounds, ybounds, var_list, dim_list): """Copy variables in var_list in subdomain [xbounds, ybounds] from oldfile to newfile. Also copies dimensions in dim_list and all global attributes. """ _copy_dimensions(oldfile, newfile, dim_list, xbounds, ybounds) _copy_variables(oldfile, newfile, var_list, xbounds, ybounds) # copy global attributes newfile.setncatts( {att: oldfile.getncattr(att) for att in oldfile.ncattrs()} ) def _copy_dimensions(oldfile, newfile, dim_list, xbounds, ybounds): """ Copy the dimensions in dims_list from oldfile to newfile. Dimensions of eta_rho, xi_rho are determined by limits of ybounds, xbounds. eta_v and xi_u have one extra because of staggering. """ dim_size_dict = { 'eta_rho': ybounds[1]-ybounds[0]+1, 'eta_u': ybounds[1]-ybounds[0]+1, 'xi_rho': xbounds[1]-xbounds[0]+1, 'xi_v': xbounds[1]-xbounds[0]+1, 'xi_u': xbounds[1]-xbounds[0], 'eta_v': ybounds[1]-ybounds[0], 'ocean_time': 0, } for dimname in dim_list: dim = oldfile.dimensions[dimname] newfile.createDimension( dimname, size=dim_size_dict.get(dimname, dim.__len__()) ) def _copy_variables(oldfile, newfile, var_list, xbounds, ybounds): """Copy variables in var_list from oldfile to newfile for subdomain [xbounds, ybounds]""" varnames_in_file = list(oldfile.variables.keys()) for varname in var_list: if varname in varnames_in_file: var = oldfile.variables[varname] dims = var.dimensions newvar = newfile.createVariable(varname, var.datatype, dims) # copy variable attributes newvar.setncatts({att: var.getncattr(att) for att in var.ncattrs()}) # fill data if 'eta_rho' in dims or 'xi_rho' in dims: newvar[:] = var[..., ybounds[0]:ybounds[1]+1, xbounds[0]:xbounds[1]+1] elif 'eta_u' in dims or 'xi_u' in dims: newvar[:] = var[..., ybounds[0]:ybounds[1]+1, xbounds[0]:xbounds[1]] elif 'eta_v' in dims or 'xi_v' in dims: newvar[:] = var[..., ybounds[0]:ybounds[1], xbounds[0]:xbounds[1]+1] else: newvar[:] = var[:] if __name__ == '__main__': get_UBC_subdomain(sys.argv[1:])