def read_nemo_oneatatime(fn_nemo_data, fn_nemo_domain, obs, landmask, chunks):
print("analyse_ssh_hourly: a")
file_list = glob.glob(fn_nemo_data)
file = file_list[0]
nemo = coast.NEMO(file, fn_nemo_domain, chunks=chunks).dataset
ind2D = gu.nearest_indices_2D(nemo.longitude,
nemo.latitude,
obs.longitude,
obs.latitude,
mask=landmask)
print("analyse_ssh_hourly: b")
nemo_list = []
for ff in range(0, len(file_list)):
file = file_list[ff]
print(file)
nemo = coast.NEMO(file, fn_nemo_domain, chunks=chunks).dataset
nemo = nemo['ssh']
nemo_ext = nemo.isel(x_dim=ind2D[0], y_dim=ind2D[1]).load()
nemo_ext = nemo_ext.swap_dims({'dim_0': 'port'})
nemo_list.append(nemo_ext)
print("analyse_ssh_hourly: c")
nemo = xr.merge(nemo_list)
print('d')
return nemo
def read_data_for_regridding_nemo(fn_nemo_data, fn_nemo_domain):
''' For reading NEMO data into the right dataset format for XESMF.
Ouput from this function must be an xarray.Dataset or xarray.DataArray
object. Longitude and latitude variables must be named 'lon' and 'lat'
respectively. If data is on rectilinear grid, there should also be
dimensions named 'lon' and 'lat'. f using, "mask" should be 1s over the
ocean and 0 over the land.
'''
import coast
# Use coast to create NEMO object and extract dataset. Only keep variables
# of interest.
ds = coast.NEMO(fn_nemo_data,
fn_nemo_domain,
multiple=True,
chunks={'season': 1})
ds = ds.dataset[['ssh', 'temperature', 'salinity']]
# Rename longitude and latitude for XESMF
ds = ds.rename({'longitude': 'lon', 'latitude': 'lat'})
# Create a landmask and place into dataset using y_dim and x_dim dimensions
# x_dim and y_dim are dimensions from the NEMO dataset object
domain = xr.open_dataset(fn_nemo_domain, chunks={})
ds['mask'] = (['y_dim', 'x_dim'], domain.top_level[0].values.astype(bool))
return ds
def read_harmonics_model_nemo(fn_nemo_harmonics, fn_nemo_domain, constituents):
'''
For reading and formatting model data. Modify or replace as necessary.
If output from this fucntion is correct then the validation script will
continue to work. Data output should be in the form of a single xarray
Dataset object. This Dataset must have the minimum form and variable names:
Dimensions: (constituent: 2, x_dim: 369, y_dim: 297)
Coordinates:
latitude (y_dim, x_dim) float32 ...
longitude (y_dim, x_dim) float32 ...
Data variables:
amplitude (constituent, y_dim, x_dim) float64 0.7484 0.7524 ... 0.0
phase (constituent, y_dim, x_dim) float64 -1.8 -1.8 ... -0.0
constituent_name (constituent) <U3 'M2' 'S2'
landmask (y_dim, x_dim) bool False False False ... True True True
Here, x_dim and y_dim are the longitude and latitude axes respectively. The
default script determines the landmask from bathymetry. If not available,
set this variable to all False (tell it there is no land -- a Lie!!).
'''
# Read in nemo harmonics using COAsT
nemo = coast.NEMO(fn_nemo_harmonics, fn_nemo_domain)
nemo = nemo.harmonics_combine(['M2', 'S2'])
# Convert to amplitude and phase.
nemo.harmonics_convert()
# Define landmask as being everywhere that the depth is 0 (or "shallower")
landmask = nemo.bathy_metry <= 0
landmask = landmask.squeeze()
nemo.dataset['landmask'] = landmask
return nemo.dataset
def read_nemo_ssh(fn_nemo_data, fn_nemo_domain, chunks):
print("analyse_ssh_hourly: Reading NEMO data")
nemo = coast.NEMO(fn_nemo_data,
fn_nemo_domain,
multiple=True,
chunks=chunks).dataset
print("analyse_ssh_hourly: Done")
return nemo[['ssh', 'time_instant']]
def read_nemo_data(self, fn_nemo_data, fn_nemo_domain, chunks):
nemo = coast.NEMO(fn_nemo_data,
fn_nemo_domain,
multiple=True,
chunks={}).dataset
nemo = nemo['ssh']
print("analyse_monthly_ssh: NEMO data read")
return nemo
def read_data_input_nemo(fn_nemo_data, fn_nemo_domain):
''' For reading multiple NEMO data files to use for analysis. Uses COAsT
to create the xarray dataset.'''
data = coast.NEMO(fn_nemo_data,
fn_nemo_domain,
multiple=True,
chunks='auto').dataset
data = data[['temperature', 'ssh', 'salinity']]
return data
def read_model_nemo(fn_nemo_data,
fn_nemo_domain,
depth_levels='all',
variables_to_extract='all'):
''' Routine for reading NEMO model data using COAsT.
This should return numpy arrays of longitude and latitude. This can be done
manually or by reading data from another file and extracting lists of
locations'''
# Read NEMO data into a COAsT object (correct format)
model_data = coast.NEMO(fn_nemo_data,
fn_nemo_domain,
grid_ref='t-grid',
multiple=True,
chunks={'time_counter': 1})
# Extract the xarray dataset and desired variables
model_data = model_data.dataset
# If dataset has a depth dimension and user has specified depth levels
if depth_levels != 'all' and 'z_dim' in model_data.dims:
model_data = model_data.isel(z_dim=depth_levels)
# If only specified variables are wanted
if variables_to_extract != 'all':
model_data = model_data[variables_to_extract]
# Create a landmask and place into dataset
# Here I create a landmask from the top_level variable in the domain file.
# This should be named 'landmask'.
domain = xr.open_dataset(fn_nemo_domain, chunks={})
model_data['landmask'] = (['y_dim', 'x_dim'],
~domain.top_level[0].values.astype(bool))
# If no mask needed, set to None (uncomment below)
# model_data['landmask'] = None
return model_data
''' # Begin by importing coast and other packages import coast import datetime import numpy as np import matplotlib.pyplot as plt # And by defining some file paths fn_nemo_dat = './example_files/COAsT_example_NEMO_data.nc' fn_nemo_dom = './example_files/COAsT_example_NEMO_domain.nc' fn_tidegauge = './example_files/tide_gauges/lowestoft-p024-uk-bodc' fn_tidegauge_mult = './example_files/tide_gauges/l*' # We need to load in a NEMO object for doing NEMO things. nemo = coast.NEMO(fn_nemo_dat, fn_nemo_dom, grid_ref='t-grid') # And now we can load in our ALTIMETRY data. By default, TIDEGAUGE is set up # to read in GESLA ASCII files. However, if no path is supplied, then the # object's dataset will be initialised as None. Custom data can then be loaded # if desired, as long as it follows the data formatting for TIDEGAUGE. Here # we load data between two specified dates: date0 = datetime.datetime(2007, 1, 10) date1 = datetime.datetime(2007, 1, 16) tidegauge = coast.TIDEGAUGE(fn_tidegauge, date_start=date0, date_end=date1) # Before comparing our observations to the model, we will interpolate a model # variable to the same time and geographical space as the tidegauge. This is # done using the obs_operator() method: tidegauge.obs_operator(nemo, mod_var_name='ssh', time_interp='nearest')
import coast
import numpy as np
import xarray as xr
import dask
import matplotlib.pyplot as plt
import matplotlib.colors as colors # colormap fiddling
#################################################
#%% Loading data
#################################################
dir_nam = "/projectsa/COAsT/NEMO_example_data/MO_INDIA/"
fil_nam = "ind_1d_cat_20180101_20180105_25hourm_grid_T.nc"
dom_nam = "domain_cfg_wcssp.nc"
sci_t = coast.NEMO(dir_nam + fil_nam, \
dir_nam + dom_nam, grid_ref='t-grid', multiple=False)
#%% Plot
fig = plt.figure()
plt.pcolormesh(sci_t.dataset.longitude, sci_t.dataset.latitude,
sci_t.dataset.temperature.isel(t_dim=0).isel(z_dim=0))
plt.xlabel('longitude')
plt.ylabel('latitude')
plt.title('WCSSP India SST')
plt.colorbar()
plt.show()
fig.savefig('WCSSP_India_SST.png', dpi=120)
import matplotlib.colors as colors # colormap fiddling
#################################################
#%% Loading data
#################################################
config = 'AMM15'
dir_nam = "/projectsa/NEMO/gmaya/2013p2/"
fil_nam = "20130415_25hourm_grid_T.nc"
dom_nam = "/projectsa/NEMO/gmaya/AMM15_GRID/amm15.mesh_mask.cs3x.nc"
chunks = {"x": 10, "y": 10, "time_counter": 10}
sci_t = coast.NEMO(dir_nam + fil_nam,
dom_nam,
grid_ref='t-grid',
multiple=False,
chunks=chunks)
# create an empty w-grid object, to store stratification
sci_w = coast.NEMO(fn_domain=dom_nam, grid_ref='w-grid', chunks=chunks)
print('* Loaded ', config, ' data')
#################################################
#%% subset of data and domain ##
#################################################
# Pick out a North Sea subdomain
print('* Extract North Sea subdomain')
ind_sci = sci_t.subset_indices([51, -4], [62, 15])
sci_nwes_t = sci_t.isel(y_dim=ind_sci[0],
try:
config = 'AMM60'
dir_AMM60 = "/projectsa/COAsT/NEMO_example_data/AMM60/"
fil_nam_AMM60 = "AMM60_1d_20100704_20100708_grid_T.nc"
mon = 'July'
#mon = 'Feb'
if mon == 'July':
fil_names_AMM60 = "AMM60_1d_201007*_grid_T.nc"
elif mon == 'Feb':
fil_names_AMM60 = "AMM60_1d_201002*_grid_T.nc"
chunks = {"x": 10, "y": 10, "time_counter": 10}
sci_t = coast.NEMO(dir_AMM60 + fil_names_AMM60,
dir_AMM60 + "mesh_mask.nc",
grid_ref='t-grid',
multiple=True,
chunks=chunks)
# create an empty w-grid object, to store stratification
sci_w = coast.NEMO(fn_domain=dir_AMM60 + "mesh_mask.nc", grid_ref='w-grid')
# OR load in AMM7 example data
except:
config = 'AMM7'
dn_files = "./example_files/"
if not os.path.isdir(dn_files):
print(
"please go download the examples file from https://linkedsystems.uk/erddap/files/COAsT_example_files/"
)
import sys
sys.path.append('/home/users/dbyrne/code/COAsT/')
import coast
import coast.general_utils as gu
import xarray as xr
import numpy as np
fn_nemo_data = "/gws/nopw/j04/jmmp_collab/CO9_AMM15/outputs/hourly/*.nc"
fn_nemo_domain = "/gws/nopw/j04/jmmp_collab/CO9_AMM15/inputs/CO7_EXACT_CFG_FILE.nc"
fn_tideanal = "/gws/nopw/j04/jmmp_collab/CO9_AMM15/obs/tideanal.edited.nc"
fn_out = "/gws/nopw/j04/jmmp_collab/CO9_AMM15/analysis/tideanal_extracted.nc"
nemo = coast.NEMO(fn_nemo_data, fn_nemo_domain, multiple=True, chunks='auto').dataset
tana = xr.open_dataset(fn_tideanal)
mask = nemo.bottom_level==0
ind2D = gu.nearest_indices_2D(nemo.longitude, nemo.latitude,
tana.longitude, tana.latitude, mask)
nemo = nemo.isel(x_dim = ind2D[0], y_dim = ind2D[1])
nemo.compute()
nemo = nemo.swap_dims({'dim_0':'port'})
nemo = nemo.swap_dims({'t_dim':'time'})
nemo.to_netcdf(fn_out)
import matplotlib.pyplot as plt
#import matplotlib.colors as colors # colormap fiddling
#################################################
#%% Loading and initialising methods ##
#################################################
dir_nam = "/projectsa/anchor/NEMO/AMM60/"
fil_nam = "AMM60_1h_20100818_20100822_NorthSea.nc"
dom_nam = "/projectsa/FASTNEt/jelt/AMM60/mesh_mask.nc"
dir_nam = '/projectsa/NEMO/jelt/AMM60_ARCHER_DUMP/AMM60smago/EXP_NSea/OUTPUT/'
fil_nam = 'AMM60_1h_20120204_20120208_NorthSea.nc'
chunks = {"x":10, "y":10, "time_counter":10}
sci_w = coast.NEMO(dir_nam + fil_nam,
dom_nam, grid_ref='w-grid', multiple=True, chunks=chunks)
sci_w.dataset = sci_w.dataset.swap_dims({'depthw':'z_dim'})
#################################################
#%% subset of data and domain ##
#################################################
# Pick out a North Sea subdomain
ind_sci = sci_w.subset_indices([51,-4], [60,15])
sci_nwes_w = sci_w.isel(y_dim=ind_sci[0], x_dim=ind_sci[1]) #nwes = northwest europe shelf
#%% Compute a diffusion from w-vel
Kz = (sci_nwes_w.dataset.wo * sci_nwes_w.dataset.e3_0).sum(dim='z_dim').mean(dim='t_dim')
# plot map
lon = sci_nwes_w.dataset.longitude.squeeze()
lat = sci_nwes_w.dataset.latitude.squeeze()
def read_nemo_ssh(self, fn_nemo_data, fn_nemo_domain, chunks):
nemo = coast.NEMO(fn_nemo_data,
fn_nemo_domain,
multiple=True,
chunks=chunks).dataset
return nemo['ssh']
def __init__(self,
fn_nemo_data,
fn_nemo_domain,
fn_en4,
fn_out,
surface_def=2,
bottom_def=10,
regional_masks=[],
region_names=[],
nemo_chunks={'time_counter': 50},
bathymetry=None):
print('0', flush=True)
nemo = coast.NEMO(fn_nemo_data,
fn_nemo_domain,
multiple=True,
chunks=nemo_chunks)
nemo_mask = nemo.dataset.bottom_level == 0
nemo.dataset = nemo.dataset.rename({'t_dim': 'time'})
if bathymetry is not None:
nemo.dataset = nemo.dataset[[
'votemper_top', 'vosaline_top', 'votemper_bot', 'vosaline_bot'
]]
else:
nemo.dataset = nemo.dataset[['votemper_top', 'vosaline_top']]
print('a', flush=True)
en4 = coast.PROFILE()
en4.read_EN4(fn_en4, multiple=True)
# Get obs in box
lonmax = np.nanmax(nemo.dataset['longitude'])
lonmin = np.nanmin(nemo.dataset['longitude'])
latmax = np.nanmax(nemo.dataset['latitude'])
latmin = np.nanmin(nemo.dataset['latitude'])
ind = coast.general_utils.subset_indices_lonlat_box(
en4.dataset['longitude'], en4.dataset['latitude'], lonmin, lonmax,
latmin, latmax)[0]
en4 = en4.isel(profile=ind)
print('b', flush=True)
# Get obs time slice
n_nemo_time = nemo.dataset.dims['time']
nemo.dataset.time.load()
en4.dataset.time.load()
nemo_time = pd.to_datetime(nemo.dataset.time.values)
en4_time = pd.to_datetime(en4.dataset.time.values)
time_max = max(nemo_time) + timedelta(hours=1)
time_min = min(nemo_time) - timedelta(hours=1)
time_ind0 = en4_time <= time_max
time_ind1 = en4_time >= time_min
time_ind = np.logical_and(time_ind0, time_ind1)
en4 = en4.isel(profile=time_ind)
# Get model indices
en4_time = pd.to_datetime(en4.dataset.time.values)
ind2D = gu.nearest_indices_2D(nemo.dataset.longitude,
nemo.dataset.latitude,
en4.dataset.longitude,
en4.dataset.latitude,
mask=nemo_mask)
print('c', flush=True)
# Estimate EN4 SST as mean of top levels
surface_ind = en4.dataset.depth <= surface_def
sst_en4 = en4.dataset.potential_temperature.where(surface_ind, np.nan)
sss_en4 = en4.dataset.practical_salinity.where(surface_ind, np.nan)
sst_en4 = sst_en4.mean(dim="z_dim", skipna=True).load()
sss_en4 = sss_en4.mean(dim="z_dim", skipna=True).load()
print('d', flush=True)
# Bottom values
if bathymetry is not None:
bathy_pts = bathymetry.isel(
x_dim=ind2D[0], y_dim=ind2D[1]).swap_dims({'dim_0': 'profile'})
bottom_ind = en4.dataset.depth >= (bathy_pts - bottom_def)
sbt_en4 = en4.dataset.potential_temperature.where(
bottom_ind, np.nan)
sbs_en4 = en4.dataset.practical_salinity.where(bottom_ind, np.nan)
sbt_en4 = sbt_en4.mean(dim="z_dim", skipna=True).load()
sbs_en4 = sbs_en4.mean(dim="z_dim", skipna=True).load()
print('e', flush=True)
# For every EN4 profile, determine the nearest model time index
# If more than t_crit away from nearest, then discard it
n_prof = en4.dataset.dims['profile']
sst_e = np.zeros(n_prof) * np.nan
sss_e = np.zeros(n_prof) * np.nan
sst_ae = np.zeros(n_prof) * np.nan
sss_ae = np.zeros(n_prof) * np.nan
crps_tem_2 = np.zeros(n_prof) * np.nan
crps_sal_2 = np.zeros(n_prof) * np.nan
crps_tem_4 = np.zeros(n_prof) * np.nan
crps_sal_4 = np.zeros(n_prof) * np.nan
crps_tem_6 = np.zeros(n_prof) * np.nan
crps_sal_6 = np.zeros(n_prof) * np.nan
sbt_e = np.zeros(n_prof) * np.nan
sbs_e = np.zeros(n_prof) * np.nan
sbt_e = np.zeros(n_prof) * np.nan
sbs_e = np.zeros(n_prof) * np.nan
# CRPS
x_dim_len = nemo.dataset.dims['x_dim']
y_dim_len = nemo.dataset.dims['y_dim']
n_r = nemo.dataset.dims['y_dim']
n_c = nemo.dataset.dims['x_dim']
regional_masks = regional_masks.copy()
region_names = region_names.copy()
regional_masks.append(np.ones((n_r, n_c)))
region_names.append('whole_domain')
n_regions = len(regional_masks)
n_season = 5
print('Starting analysis')
for tii in range(0, n_nemo_time):
print(nemo_time[tii], flush=True)
time_diff = np.abs(nemo_time[tii] -
en4_time).astype('timedelta64[m]')
use_ind = np.where(time_diff.astype(int) < 30)[0]
n_use = len(use_ind)
if n_use > 0:
tmp = nemo.isel(time=tii).dataset
tmp.load()
x_tmp = ind2D[0][use_ind]
y_tmp = ind2D[1][use_ind]
x_tmp = xr.where(x_tmp < x_dim_len - 7, x_tmp, np.nan)
y_tmp = xr.where(y_tmp < y_dim_len - 7, y_tmp, np.nan)
x_tmp = xr.where(x_tmp > 7, x_tmp, np.nan)
y_tmp = xr.where(y_tmp > 7, y_tmp, np.nan)
shared_mask = np.logical_or(np.isnan(x_tmp), np.isnan(y_tmp))
shared_mask = np.where(~shared_mask)
x_tmp = x_tmp[shared_mask].astype(int)
y_tmp = y_tmp[shared_mask].astype(int)
use_ind = use_ind[shared_mask].astype(int)
n_use = len(use_ind)
if n_use < 1:
continue
tmp_pts = tmp.isel(x_dim=x_tmp, y_dim=y_tmp)
sst_en4_tmp = sst_en4.values[use_ind]
sss_en4_tmp = sss_en4.values[use_ind]
sst_e[use_ind] = tmp_pts.votemper_top.values - sst_en4_tmp
sss_e[use_ind] = tmp_pts.vosaline_top.values - sss_en4_tmp
if bathymetry is not None:
sbt_en4_tmp = sbt_en4.values[use_ind]
sbs_en4_tmp = sbs_en4.values[use_ind]
sbt_e[use_ind] = tmp_pts.votemper_bot.values - sbt_en4_tmp
sbs_e[use_ind] = tmp_pts.vosaline_bot.values - sbs_en4_tmp
nh_x = [
np.arange(x_tmp[ii] - 2, x_tmp[ii] + 3)
for ii in range(0, n_use)
]
nh_y = [
np.arange(y_tmp[ii] - 2, y_tmp[ii] + 3)
for ii in range(0, n_use)
]
nh = [
tmp.isel(x_dim=nh_x[ii], y_dim=nh_y[ii])
for ii in range(0, n_use)
]
crps_tem_tmp = [
cu.crps_empirical(nh[ii].votemper_top.values.flatten(),
sst_en4_tmp[ii])
for ii in range(0, n_use)
]
crps_sal_tmp = [
cu.crps_empirical(nh[ii].vosaline_top.values.flatten(),
sss_en4_tmp[ii])
for ii in range(0, n_use)
]
crps_tem_2[use_ind] = crps_tem_tmp
crps_sal_2[use_ind] = crps_sal_tmp
nh_x = [
np.arange(x_tmp[ii] - 4, x_tmp[ii] + 5)
for ii in range(0, n_use)
]
nh_y = [
np.arange(y_tmp[ii] - 4, y_tmp[ii] + 5)
for ii in range(0, n_use)
]
nh = [
tmp.isel(x_dim=nh_x[ii], y_dim=nh_y[ii])
for ii in range(0, n_use)
]
crps_tem_tmp = [
cu.crps_empirical(nh[ii].votemper_top.values.flatten(),
sst_en4_tmp[ii])
for ii in range(0, n_use)
]
crps_sal_tmp = [
cu.crps_empirical(nh[ii].vosaline_top.values.flatten(),
sss_en4_tmp[ii])
for ii in range(0, n_use)
]
crps_tem_4[use_ind] = crps_tem_tmp
crps_sal_4[use_ind] = crps_sal_tmp
nh_x = [
np.arange(x_tmp[ii] - 6, x_tmp[ii] + 7)
for ii in range(0, n_use)
]
nh_y = [
np.arange(y_tmp[ii] - 6, y_tmp[ii] + 7)
for ii in range(0, n_use)
]
nh = [
tmp.isel(x_dim=nh_x[ii], y_dim=nh_y[ii])
for ii in range(0, n_use)
]
crps_tem_tmp = [
cu.crps_empirical(nh[ii].votemper_top.values.flatten(),
sst_en4_tmp[ii])
for ii in range(0, n_use)
]
crps_sal_tmp = [
cu.crps_empirical(nh[ii].vosaline_top.values.flatten(),
sss_en4_tmp[ii])
for ii in range(0, n_use)
]
crps_tem_6[use_ind] = crps_tem_tmp
crps_sal_6[use_ind] = crps_sal_tmp
print('Profile analysis done', flush=True)
sst_ae = np.abs(sst_e)
sss_ae = np.abs(sss_e)
sbt_ae = np.abs(sbt_e)
sbs_ae = np.abs(sbs_e)
# Put everything into xarray dataset
en4_season = get_season_index(sst_en4.time.values)
# Regional Means
reg_array = np.zeros((n_regions, n_season)) * np.nan
is_in_region = [mm[ind2D[1], ind2D[0]] for mm in regional_masks]
is_in_region = np.array(is_in_region, dtype=bool)
ds = xr.Dataset(coords=dict(longitude=("profile",
sst_en4.longitude.values),
latitude=("profile",
sst_en4.latitude.values),
time=("profile", sst_en4.time.values),
season_ind=("profile", en4_season)),
data_vars=dict(obs_sst=('profile', sst_en4.values),
obs_sss=('profile', sss_en4.values),
sst_err=("profile", sst_e),
sss_err=("profile", sss_e),
sst_abs_err=("profile", sst_ae),
sss_abs_err=("profile", sss_ae),
sst_crps2=("profile", crps_tem_2),
sss_crps2=("profile", crps_sal_2),
sst_crps4=("profile", crps_tem_4),
sss_crps4=("profile", crps_sal_4),
sst_crps6=("profile", crps_tem_6),
sss_crps6=("profile", crps_sal_6)))
season_names = ['All', 'DJF', 'MAM', 'JJA', 'SON']
ds = ds.chunk({'profile': 10000})
ds_mean = xr.Dataset(
coords=dict(longitude=("profile", sst_en4.longitude.values),
latitude=("profile", sst_en4.latitude.values),
time=("profile", sst_en4.time.values),
season_ind=("profile", en4_season),
region_names=('region', region_names),
season=('season', season_names)),
data_vars=dict(sst_me=(["region", "season"], reg_array.copy()),
sss_me=(["region", "season"], reg_array.copy()),
sst_mae=(["region", "season"], reg_array.copy()),
sss_mae=(["region", "season"], reg_array.copy()),
sst_crps2_mean=(["region",
"season"], reg_array.copy()),
sss_crps2_mean=(["region",
"season"], reg_array.copy()),
sst_crps4_mean=(["region",
"season"], reg_array.copy()),
sss_crps4_mean=(["region",
"season"], reg_array.copy()),
sst_crps6_mean=(["region",
"season"], reg_array.copy()),
sss_crps6_mean=(["region",
"season"], reg_array.copy())))
if bathymetry is not None:
ds_mean['sbt_me'] = (['region', 'season'], reg_array.copy())
ds_mean['sbs_me'] = (['region', 'season'], reg_array.copy())
ds_mean['sbt_mae'] = (['region', 'season'], reg_array.copy())
ds_mean['sbs_mae'] = (['region', 'season'], reg_array.copy())
ds['obs_sbt'] = (['profile'], sbt_en4.values)
ds['obs_sbs'] = (['profile'], sbs_en4.values)
ds['sbt_err'] = (['profile'], sbt_e)
ds['sbs_err'] = (['profile'], sbs_e)
ds['sbt_abs_err'] = (['profile'], sbt_ae)
ds['sbs_abs_err'] = (['profile'], sbs_ae)
for reg in range(0, n_regions):
reg_ind = np.where(is_in_region[reg].astype(bool))[0]
ds_reg = ds.isel(profile=reg_ind)
ds_reg_group = ds_reg.groupby('time.season')
ds_reg_mean = ds_reg_group.mean(skipna=True).compute()
ds_mean['sst_me'][reg, 1:] = ds_reg_mean.sst_err.values
ds_mean['sss_me'][reg, 1:] = ds_reg_mean.sss_err.values
ds_mean['sst_mae'][reg, 1:] = ds_reg_mean.sst_abs_err.values
ds_mean['sss_mae'][reg, 1:] = ds_reg_mean.sss_abs_err.values
ds_mean['sst_crps2_mean'][reg, 1:] = ds_reg_mean.sst_crps2.values
ds_mean['sss_crps2_mean'][reg, 1:] = ds_reg_mean.sss_crps2.values
ds_mean['sst_crps4_mean'][reg, 1:] = ds_reg_mean.sst_crps4.values
ds_mean['sss_crps4_mean'][reg, 1:] = ds_reg_mean.sss_crps4.values
ds_mean['sst_crps6_mean'][reg, 1:] = ds_reg_mean.sst_crps6.values
ds_mean['sss_crps6_mean'][reg, 1:] = ds_reg_mean.sss_crps6.values
if bathymetry is not None:
ds_mean['sbt_me'][reg, 1:] = ds_reg_mean.sbt_err.values
ds_mean['sbs_me'][reg, 1:] = ds_reg_mean.sbs_err.values
ds_mean['sbt_mae'][reg, 1:] = ds_reg_mean.sbt_abs_err.values
ds_mean['sbs_mae'][reg, 1:] = ds_reg_mean.sbs_abs_err.values
ds_reg_mean = ds_reg.mean(dim='profile', skipna=True).compute()
ds_mean['sst_me'][reg, 0] = ds_reg_mean.sst_err.values
ds_mean['sss_me'][reg, 0] = ds_reg_mean.sss_err.values
ds_mean['sst_mae'][reg, 0] = ds_reg_mean.sst_abs_err.values
ds_mean['sss_mae'][reg, 0] = ds_reg_mean.sss_abs_err.values
ds_mean['sst_crps2_mean'][reg, 0] = ds_reg_mean.sst_crps2.values
ds_mean['sss_crps2_mean'][reg, 0] = ds_reg_mean.sss_crps2.values
ds_mean['sst_crps4_mean'][reg, 0] = ds_reg_mean.sst_crps4.values
ds_mean['sss_crps4_mean'][reg, 0] = ds_reg_mean.sss_crps4.values
ds_mean['sst_crps6_mean'][reg, 0] = ds_reg_mean.sst_crps6.values
ds_mean['sss_crps6_mean'][reg, 0] = ds_reg_mean.sss_crps6.values
if bathymetry is not None:
ds_mean['sbt_me'][reg, 0] = ds_reg_mean.sbt_err.values
ds_mean['sbs_me'][reg, 0] = ds_reg_mean.sbs_err.values
ds_mean['sbt_mae'][reg, 0] = ds_reg_mean.sbt_abs_err.values
ds_mean['sbs_mae'][reg, 0] = ds_reg_mean.sbs_abs_err.values
ds_out = xr.merge((ds, ds_mean))
ds_out['is_in_region'] = (['region', 'profile'], is_in_region)
# Write to file
write_ds_to_file(ds_out, fn_out)
import numpy as np
import xarray as xr
import dask
import matplotlib.pyplot as plt
import matplotlib.colors as colors # colormap fiddling
#################################################
#%% Loading data
#################################################
dir_nam = "/projectsa/accord/GCOMS1k/OUTPUTS/BLZE12_02/2015/"
fil_nam = "BLZE12_1h_20151101_20151130_grid_T.nc"
dom_nam = "/projectsa/accord/GCOMS1k/INPUTS/BLZE12_C1/domain_cfg.nc"
sci_t = coast.NEMO(dir_nam + fil_nam, \
dom_nam, grid_ref='t-grid', multiple=False)
sci_u = coast.NEMO(dir_nam + fil_nam.replace('grid_T','grid_U'), \
dom_nam, grid_ref='u-grid', multiple=False)
sci_v = coast.NEMO(dir_nam + fil_nam.replace('grid_T','grid_V'), \
dom_nam, grid_ref='v-grid', multiple=False)
# create an empty w-grid object, to store stratification
sci_w = coast.NEMO(fn_domain=dom_nam, grid_ref='w-grid')
#%% Plot
plt.pcolormesh(sci_t.dataset.ssh.isel(t_dim=0))
plt.show()