def make_obcs (location, grid_path, input_path, output_dir, source='SOSE', use_seaice=True, nc_out=None, prec=32, split=180):
from grid import SOSEGrid
from file_io import NCfile, read_netcdf
from interpolation import interp_bdry
if source == 'SOSE':
input_path = real_dir(input_path)
output_dir = real_dir(output_dir)
# Fields to interpolate
# Important: SIarea has to be before SIuice and SIvice so it can be used for masking
fields = ['THETA', 'SALT', 'UVEL', 'VVEL', 'SIarea', 'SIheff', 'SIuice', 'SIvice', 'ETAN']
# Flag for 2D or 3D
dim = [3, 3, 3, 3, 2, 2, 2, 2, 2]
# Flag for grid type
gtype = ['t', 't', 'u', 'v', 't', 't', 'u', 'v', 't']
if source == 'MIT':
# Also consider snow thickness
fields += ['SIhsnow']
dim += [2]
gtype += ['t']
# End of filenames for input
infile_tail = '_climatology.data'
# End of filenames for output
outfile_tail = '_'+source+'.OBCS_'+location
print 'Building MITgcm grid'
if source == 'SOSE':
model_grid = grid_check_split(grid_path, split)
elif source == 'MIT':
model_grid = Grid(grid_path)
# Figure out what the latitude or longitude is on the boundary, both on the centres and outside edges of those cells
if location == 'S':
lat0 = model_grid.lat_1d[0]
lat0_e = model_grid.lat_corners_1d[0]
print 'Southern boundary at ' + str(lat0) + ' (cell centre), ' + str(lat0_e) + ' (cell edge)'
elif location == 'N':
lat0 = model_grid.lat_1d[-1]
lat0_e = 2*model_grid.lat_corners_1d[-1] - model_grid.lat_corners_1d[-2]
print 'Northern boundary at ' + str(lat0) + ' (cell centre), ' + str(lat0_e) + ' (cell edge)'
elif location == 'W':
lon0 = model_grid.lon_1d[0]
lon0_e = model_grid.lon_corners_1d[0]
print 'Western boundary at ' + str(lon0) + ' (cell centre), ' + str(lon0_e) + ' (cell edge)'
elif location == 'E':
lon0 = model_grid.lon_1d[-1]
lon0_e = 2*model_grid.lon_corners_1d[-1] - model_grid.lon_corners_1d[-2]
print 'Eastern boundary at ' + str(lon0) + ' (cell centre), ' + str(lon0_e) + ' (cell edge)'
else:
print 'Error (make_obcs): invalid location ' + str(location)
sys.exit()
if source == 'SOSE':
print 'Building SOSE grid'
source_grid = SOSEGrid(input_path+'grid/', model_grid=model_grid, split=split)
elif source == 'MIT':
print 'Building grid from source model'
source_grid = Grid(input_path)
else:
print 'Error (make_obcs): invalid source ' + source
sys.exit()
# Calculate interpolation indices and coefficients to the boundary latitude or longitude
if location in ['N', 'S']:
# Cell centre
j1, j2, c1, c2 = interp_slice_helper(source_grid.lat_1d, lat0)
# Cell edge
j1_e, j2_e, c1_e, c2_e = interp_slice_helper(source_grid.lat_corners_1d, lat0_e)
else:
# Pass lon=True to consider the possibility of boundary near 0E
i1, i2, c1, c2 = interp_slice_helper(source_grid.lon_1d, lon0, lon=True)
i1_e, i2_e, c1_e, c2_e = interp_slice_helper(source_grid.lon_corners_1d, lon0_e, lon=True)
# Set up a NetCDF file so the user can check the results
if nc_out is not None:
ncfile = NCfile(nc_out, model_grid, 'xyzt')
ncfile.add_time(np.arange(12)+1, units='months')
# Process fields
for n in range(len(fields)):
if fields[n].startswith('SI') and not use_seaice:
continue
print 'Processing ' + fields[n]
if source == 'SOSE':
in_file = input_path + fields[n] + infile_tail
out_file = output_dir + fields[n] + outfile_tail
# Read the monthly climatology at all points
if source == 'SOSE':
if dim[n] == 3:
source_data = source_grid.read_field(in_file, 'xyzt')
else:
source_data = source_grid.read_field(in_file, 'xyt')
else:
source_data = read_netcdf(input_path, fields[n])
if fields[n] == 'SIarea' and source == 'SOSE':
# We'll need this field later for SIuice and SIvice, as SOSE didn't mask those variables properly
print 'Interpolating sea ice area to u and v grids for masking of sea ice velocity'
source_aice_u = interp_grid(source_data, source_grid, 't', 'u', time_dependent=True, mask_with_zeros=True, periodic=True)
source_aice_v = interp_grid(source_data, source_grid, 't', 'v', time_dependent=True, mask_with_zeros=True, periodic=True)
# Set sea ice velocity to zero wherever sea ice area is zero
if fields[n] in ['SIuice', 'SIvice'] and source == 'SOSE':
print 'Masking sea ice velocity with sea ice area'
if fields[n] == 'SIuice':
index = source_aice_u==0
else:
index = source_aice_v==0
source_data[index] = 0
# Choose the correct grid for lat, lon, hfac
source_lon, source_lat = source_grid.get_lon_lat(gtype=gtype[n], dim=1)
source_hfac = source_grid.get_hfac(gtype=gtype[n])
model_lon, model_lat = model_grid.get_lon_lat(gtype=gtype[n], dim=1)
model_hfac = model_grid.get_hfac(gtype=gtype[n])
# Interpolate to the correct grid and choose the correct horizontal axis
if location in ['N', 'S']:
if gtype[n] == 'v':
source_data = c1_e*source_data[...,j1_e,:] + c2_e*source_data[...,j2_e,:]
# Multiply hfac by the ceiling of hfac on each side, to make sure we're not averaging over land
source_hfac = (c1_e*source_hfac[...,j1_e,:] + c2_e*source_hfac[...,j2_e,:])*np.ceil(source_hfac[...,j1_e,:])*np.ceil(source_hfac[...,j2_e,:])
else:
source_data = c1*source_data[...,j1,:] + c2*source_data[...,j2,:]
source_hfac = (c1*source_hfac[...,j1,:] + c2*source_hfac[...,j2,:])*np.ceil(source_hfac[...,j1,:])*np.ceil(source_hfac[...,j2,:])
source_haxis = source_lon
model_haxis = model_lon
if location == 'S':
model_hfac = model_hfac[:,0,:]
else:
model_hfac = model_hfac[:,-1,:]
else:
if gtype[n] == 'u':
source_data = c1_e*source_data[...,i1_e] + c2_e*source_data[...,i2_e]
source_hfac = (c1_e*source_hfac[...,i1_e] + c2_e*source_hfac[...,i2_e])*np.ceil(source_hfac[...,i1_e])*np.ceil(source_hfac[...,i2_e])
else:
source_data = c1*source_data[...,i1] + c2*source_data[...,i2]
source_hfac = (c1*source_hfac[...,i1] + c2*source_hfac[...,i2])*np.ceil(source_hfac[...,i1])*np.ceil(source_hfac[...,i2])
source_haxis = source_lat
model_haxis = model_lat
if location == 'W':
model_hfac = model_hfac[...,0]
else:
model_hfac = model_hfac[...,-1]
if source == 'MIT' and model_haxis[0] < source_haxis[0]:
# Need to extend source data to the west or south. Just add one row.
source_haxis = np.concatenate(([model_haxis[0]-0.1], source_haxis))
source_data = np.concatenate((np.expand_dims(source_data[:,...,0], -1), source_data), axis=-1)
source_hfac = np.concatenate((np.expand_dims(source_hfac[:,0], 1), source_hfac), axis=1)
# For 2D variables, just need surface hfac
if dim[n] == 2:
source_hfac = source_hfac[0,:]
model_hfac = model_hfac[0,:]
# Now interpolate each month to the model grid
if dim[n] == 3:
data_interp = np.zeros([12, model_grid.nz, model_haxis.size])
else:
data_interp = np.zeros([12, model_haxis.size])
for month in range(12):
print '...interpolating month ' + str(month+1)
data_interp_tmp = interp_bdry(source_haxis, source_grid.z, source_data[month,:], source_hfac, model_haxis, model_grid.z, model_hfac, depth_dependent=(dim[n]==3))
if fields[n] not in ['THETA', 'SALT']:
# Zero in land mask is more physical than extrapolated data
index = model_hfac==0
data_interp_tmp[index] = 0
data_interp[month,:] = data_interp_tmp
write_binary(data_interp, out_file, prec=prec)
if nc_out is not None:
print '...adding to ' + nc_out
# Construct the dimension code
if location in ['S', 'N']:
dimension = 'x'
else:
dimension = 'y'
if dim[n] == 3:
dimension += 'z'
dimension += 't'
ncfile.add_variable(fields[n] + '_' + location, data_interp, dimension)
if nc_out is not None:
ncfile.close()
def sose_ics (grid_path, sose_dir, output_dir, nc_out=None, constant_t=-1.9, constant_s=34.4, split=180, prec=64):
from grid import SOSEGrid
from file_io import NCfile
from interpolation import interp_reg
sose_dir = real_dir(sose_dir)
output_dir = real_dir(output_dir)
# Fields to interpolate
fields = ['THETA', 'SALT', 'SIarea', 'SIheff']
# Flag for 2D or 3D
dim = [3, 3, 2, 2]
# Constant values for ice shelf cavities
constant_value = [constant_t, constant_s, 0, 0]
# End of filenames for input
infile_tail = '_climatology.data'
# End of filenames for output
outfile_tail = '_SOSE.ini'
print 'Building grids'
# First build the model grid and check that we have the right value for split
model_grid = grid_check_split(grid_path, split)
# Now build the SOSE grid
sose_grid = SOSEGrid(sose_dir+'grid/', model_grid=model_grid, split=split)
# Extract land mask
sose_mask = sose_grid.hfac == 0
print 'Building mask for SOSE points to fill'
# Figure out which points we need for interpolation
# Find open cells according to the model, interpolated to SOSE grid
model_open = np.ceil(interp_reg(model_grid, sose_grid, np.ceil(model_grid.hfac), fill_value=1))
# Find ice shelf cavity points according to model, interpolated to SOSE grid
model_cavity = np.ceil(interp_reg(model_grid, sose_grid, xy_to_xyz(model_grid.ice_mask, model_grid), fill_value=0)).astype(bool)
# Select open, non-cavity cells
fill = model_open*np.invert(model_cavity)
# Extend into the mask a few times to make sure there are no artifacts near the coast
fill = extend_into_mask(fill, missing_val=0, use_3d=True, num_iters=3)
# Set up a NetCDF file so the user can check the results
if nc_out is not None:
ncfile = NCfile(nc_out, model_grid, 'xyz')
# Process fields
for n in range(len(fields)):
print 'Processing ' + fields[n]
in_file = sose_dir + fields[n] + infile_tail
out_file = output_dir + fields[n] + outfile_tail
print '...reading ' + in_file
# Just keep the January climatology
if dim[n] == 3:
sose_data = sose_grid.read_field(in_file, 'xyzt')[0,:]
else:
# Fill any missing regions with zero sea ice, as we won't be extrapolating them later
sose_data = sose_grid.read_field(in_file, 'xyt', fill_value=0)[0,:]
# Discard the land mask, and extrapolate slightly into missing regions so the interpolation doesn't get messed up.
print '...extrapolating into missing regions'
if dim[n] == 3:
sose_data = discard_and_fill(sose_data, sose_mask, fill)
# Fill cavity points with constant values
sose_data[model_cavity] = constant_value[n]
else:
# Just care about surface layer
sose_data = discard_and_fill(sose_data, sose_mask[0,:], fill[0,:], use_3d=False)
print '...interpolating to model grid'
data_interp = interp_reg(sose_grid, model_grid, sose_data, dim=dim[n])
# Fill the land mask with zeros
if dim[n] == 3:
data_interp[model_grid.hfac==0] = 0
else:
data_interp[model_grid.hfac[0,:]==0] = 0
write_binary(data_interp, out_file, prec=prec)
if nc_out is not None:
print '...adding to ' + nc_out
if dim[n] == 3:
ncfile.add_variable(fields[n], data_interp, 'xyz')
else:
ncfile.add_variable(fields[n], data_interp, 'xy')
if nc_out is not None:
ncfile.close()
def sose_sss_restoring (grid_path, sose_dir, output_salt_file, output_mask_file, nc_out=None, h0=-1250, obcs_sponge=0, split=180, prec=64):
sose_dir = real_dir(sose_dir)
print 'Building grids'
# First build the model grid and check that we have the right value for split
model_grid = grid_check_split(grid_path, split)
# Now build the SOSE grid
sose_grid = SOSEGrid(sose_dir+'grid/', model_grid=model_grid, split=split)
# Extract surface land mask
sose_mask = sose_grid.hfac[0,:] == 0
print 'Building mask'
mask_surface = np.ones([model_grid.ny, model_grid.nx])
# Mask out land and ice shelves
mask_surface[model_grid.hfac[0,:]==0] = 0
# Save this for later
mask_land_ice = np.copy(mask_surface)
# Mask out continental shelf
mask_surface[model_grid.bathy > h0] = 0
# Smooth, and remask the land and ice shelves
mask_surface = smooth_xy(mask_surface, sigma=2)*mask_land_ice
if obcs_sponge > 0:
# Also mask the cells affected by OBCS and/or its sponge
mask_surface[:obcs_sponge,:] = 0
mask_surface[-obcs_sponge:,:] = 0
mask_surface[:,:obcs_sponge] = 0
mask_surface[:,-obcs_sponge:] = 0
# Make a 3D version with zeros in deeper layers
mask_3d = np.zeros([model_grid.nz, model_grid.ny, model_grid.nx])
mask_3d[0,:] = mask_surface
print 'Reading SOSE salinity'
# Just keep the surface layer
sose_sss = sose_grid.read_field(sose_dir+'SALT_climatology.data', 'xyzt')[:,0,:,:]
# Figure out which SOSE points we need for interpolation
# Restoring mask interpolated to the SOSE grid
fill = np.ceil(interp_reg(model_grid, sose_grid, mask_3d[0,:], dim=2, fill_value=1))
# Extend into the mask a few times to make sure there are no artifacts near the coast
fill = extend_into_mask(fill, missing_val=0, num_iters=3)
# Process one month at a time
sss_interp = np.zeros([12, model_grid.nz, model_grid.ny, model_grid.nx])
for month in range(12):
print 'Month ' + str(month+1)
print '...filling missing values'
sose_sss_filled = discard_and_fill(sose_sss[month,:], sose_mask, fill, use_3d=False)
print '...interpolating'
# Mask out land and ice shelves
sss_interp[month,0,:] = interp_reg(sose_grid, model_grid, sose_sss_filled, dim=2)*mask_land_ice
write_binary(sss_interp, output_salt_file, prec=prec)
write_binary(mask_3d, output_mask_file, prec=prec)
if nc_out is not None:
print 'Writing ' + nc_out
ncfile = NCfile(nc_out, model_grid, 'xyzt')
ncfile.add_time(np.arange(12)+1, units='months')
ncfile.add_variable('salinity', sss_interp, 'xyzt', units='psu')
ncfile.add_variable('restoring_mask', mask_3d, 'xyz')
ncfile.close()