def operate(self, vid: str,
variable: xa.DataArray) -> Dict[str, xa.DataArray]:
"""
Convenience method defined for this particular operation
"""
opSpecs = self.request['operation']
result_arrays: Dict[str, xa.DataArray] = {}
for opSpec in opSpecs:
opId = opSpec['name'].split(':')[1]
opAxis = opSpec['axis']
coslat = np.cos(np.deg2rad(variable.coords['latitude'].values))
wgts = np.sqrt(coslat)[..., np.newaxis]
solver = Eof(variable, weights=wgts)
if opId == "correlation":
result_arrays = solver.eofsAsCorrelation(neofs=1)
elif opId == "covariance":
result_arrays = solver.eofsAsCovariance(neofs=1)
else:
raise Exception(f"Unknown operation for EOF: '{opId}'")
return result_arrays
# Read SST anomalies using the xarray module. The file contains November-March
# averages of SST anomaly in the central and northern Pacific.
filename = example_data_path('sst_ndjfm_anom.nc')
sst = xr.open_dataset(filename)['sst']
# Create an EOF solver to do the EOF analysis. Square-root of cosine of
# latitude weights are applied before the computation of EOFs.
coslat = np.cos(np.deg2rad(sst.coords['latitude'].values))
wgts = np.sqrt(coslat)[..., np.newaxis]
solver = Eof(sst, weights=wgts)
# Retrieve the leading EOF, expressed as the correlation between the leading
# PC time series and the input SST anomalies at each grid point, and the
# leading PC time series itself.
eof1 = solver.eofsAsCorrelation(neofs=1)
pc1 = solver.pcs(npcs=1, pcscaling=1)
# Plot the leading EOF expressed as correlation in the Pacific domain.
clevs = np.linspace(-1, 1, 11)
ax = plt.axes(projection=ccrs.PlateCarree(central_longitude=190))
fill = eof1[0].plot.contourf(ax=ax, levels=clevs, cmap=plt.cm.RdBu_r,
add_colorbar=False, transform=ccrs.PlateCarree())
ax.add_feature(cfeature.LAND, facecolor='w', edgecolor='k')
cb = plt.colorbar(fill, orientation='horizontal')
cb.set_label('correlation coefficient', fontsize=12)
ax.set_title('EOF1 expressed as correlation', fontsize=16)
# Plot the leading PC time series.
plt.figure()
pc1[:, 0].plot(color='b', linewidth=2)
)['psl'] #units Pa
psl = psl.sel(time=slice(start, end))
psl_obs = xr.open_dataset('processed_data/remap-woa09_psl_Amon_ERA-Int.nc')[
'psl'] #units Pa
psl_obs = psl_obs.sel(time=slice(start, end))
# In[246]:
psl_sof20s = psl.sel(lat=slice(-90, -20))
psl_sof20s = psl_sof20s - psl_sof20s.mean(dim='time')
coslat = np.cos(np.deg2rad(psl_sof20s.coords['lat'].values)).clip(0., 1.)
wgts = np.sqrt(coslat)[..., np.newaxis]
#psl_sof20s
solver = Eof(psl_sof20s, weights=wgts)
sh_eof = solver.eofsAsCorrelation(neofs=1)
var_s = solver.varianceFraction(neigs=1)
psl_sof20s_obs = psl_obs.sel(lat=slice(-90, -20))
psl_sof20s_obs = psl_sof20s_obs - psl_sof20s_obs.mean(dim='time')
#psl_sof20s
solver_obs = Eof(psl_sof20s_obs, weights=wgts)
sh_eof_obs = solver_obs.eofsAsCorrelation(neofs=1)
var_s_obs = solver_obs.varianceFraction(neigs=1)
# In[247]:
import iris
import iris.coord_categorisation
cube = iris.load_cube(
def eof_orca_latlon_box(run, var, modes, lon_bnds, lat_bnds, pathfile, plot,
time, eoftype):
if (var == 'temp'):
key = 'votemper'
key1 = "votemper"
elif (var == 'sal'):
key = 'vosaline'
key1 = "vosaline"
elif (var == 'MLD'):
key = 'somxl010'
key1 = "somxl010"
# read data
ds = xr.open_dataset(pathfile)
#ds["time_counter"] = ds['time_counter']+(np.datetime64('0002-01-01')-np.datetime64('0001-01-01'))
if time == 'comparison':
ds = ds.sel(time_counter=slice('1958-01-01', '2006-12-31'))
# cut box for EOF at surface
if var == 'MLD':
data = ds[key].sel(lon=slice(lon_bnds[0], lon_bnds[1]),
lat=slice(lat_bnds[0], lat_bnds[1]))
#data = cut_latlon_box(ds[key][:,:,:],ds.lon,ds.lat,
# lon_bnds,lat_bnds)
else:
data = ds[key][:, 0, :, :].sel(lon=slice(lon_bnds[0], lon_bnds[1]),
lat=slice(lat_bnds[0], lat_bnds[1]))
#data = cut_latlon_box(ds[key][:,0,:,:],ds.lon,ds.lat,
# lon_bnds,lat_bnds)
data = data.to_dataset()
# detrend data
data[key1] = (['time_counter', 'lat', 'lon'],
signal.detrend(data[key].fillna(0), axis=0, type='linear'))
#data=data.where(data!=0)
# remove seasonal cycle and drop unnecessary coordinates
if 'time_centered' in list(data.coords):
data = deseason_month(data).drop('month').drop(
'time_centered') # somehow pca doesn't work otherwise
else:
data = deseason_month(data).drop(
'month') # somehow pca doesn't work otherwise
# set 0 values back to nan
data = data.where(data != 0)
# EOF analysis
#Square-root of cosine of latitude weights are applied before the computation of EOFs.
coslat = np.cos(np.deg2rad(data['lat'].values))
coslat, _ = np.meshgrid(coslat, np.arange(0, len(data['lon'])))
wgts = np.sqrt(coslat)
solver = Eof(data[key], weights=wgts.transpose())
pcs = solver.pcs(npcs=modes, pcscaling=1)
if eoftype == 'correlation':
eof = solver.eofsAsCorrelation(neofs=modes)
elif eoftype == 'covariance':
eof = solver.eofsAsCovariance(neofs=modes)
else:
eof = solver.eofs(neofs=modes)
varfr = solver.varianceFraction(neigs=4)
print(varfr)
#----------- Plotting --------------------
plt.close("all")
if plot == 1:
for i in np.arange(0, modes):
fig = plt.figure(figsize=(8, 2))
ax1 = fig.add_axes([0.1, 0.1, 0.3, 0.9],
projection=ccrs.PlateCarree()) # main axes
ax1.set_extent(
(lon_bnds[0], lon_bnds[1], lat_bnds[0], lat_bnds[1]))
# discrete colormap
cmap = plt.get_cmap('RdYlBu',
len(np.arange(10, 30)) -
1) #inferno similar to cmo thermal
eof[i, :, :].plot(ax=ax1,
cbar_kwargs={'label': 'Correlation'},
transform=ccrs.PlateCarree(),
x='lon',
y='lat',
add_colorbar=True,
cmap=cmap)
gl = map_stuff(ax1)
gl.xlocator = mticker.FixedLocator([100, 110, 120])
gl.ylocator = mticker.FixedLocator(np.arange(-35, -10, 5))
plt.text(116,
-24,
str(np.round(varfr[i].values, decimals=2)),
horizontalalignment='center',
verticalalignment='center',
transform=ccrs.PlateCarree(),
fontsize=8)
ax2 = fig.add_axes([0.5, 0.1, 0.55, 0.9]) # main axes
plt.plot(pcs.time_counter,
pcs[:, i].values,
linewidth=0.1,
color='k')
anomaly(ax2, pcs.time_counter.values, pcs.values[:, i], [0, 0])
ax2.set_xlim(
[pcs.time_counter[0].values, pcs.time_counter[-1].values])
plt.savefig(pathplots + 'eof_as' + eoftype + '_mode' + str(i) +
'_' + time + '_' + run + '_' + var + '.png',
dpi=300,
bbox_inches='tight',
pad_inches=0.1)
plt.show()
#----------------------------------------------
return pcs, eof, varfr
from eofs.xarray import Eof
# --- read netcdf file
dset = xr.open_dataset('asstdt_pacific.nc')
# --- select djf months
sst = dset['sst'].sel(time=np.in1d(dset['time.month'], [1, 2, 12]))
# --- square-root of cosine of latitude weights
coslat = np.cos(np.deg2rad(sst.coords['lat'].values))
wgts = np.sqrt(coslat)[..., np.newaxis]
# --- eof solver
solver = Eof(sst, weights=wgts)
# --- eof results
eofs = solver.eofsAsCorrelation(neofs=2)
pcs = solver.pcs(npcs=2, pcscaling=1)
variance_fractions = solver.varianceFraction()
north_test = solver.northTest(vfscaled=True)
# --- spatial patterns
fig, ax = plot.subplots(axwidth=5, nrows=2, tight=True, proj='pcarree',
proj_kw={'lon_0': 180})
# --- format options
ax.format(land=False, coast=True, innerborders=True, borders=True,
large='15px', labels=False,
latlim=(31, -31), lonlim=(119, 291),
geogridlinewidth=0,
abcloc='ul')
# a) first EOF mode
def main():
ens = sys.argv[1]
sYear = sys.argv[2]
eYear = sys.argv[3]
if int(sYear) < 1920:
raise ValueError("Starting year must be 1920 or later.")
if int(eYear) > 2100:
raise ValueError("End year must be 2100 or earlier.")
print("Computing NPGO for ensemble number " + ens + "...")
filepath = ('/glade/scratch/rbrady/EBUS_BGC_Variability/' +
'global_residuals/SST/remapped/remapped.SST.' + ens +
'.192001-210012.nc')
print("Global residuals loaded...")
ds = xr.open_dataset(filepath)
ds = ds['SST'].squeeze()
# Make time dimension readable through xarray.
ds['time'] = pd.date_range('1920-01', '2101-01', freq='M')
# Reduce to time period of interest.
ds = ds.sel(time=slice(sYear + '-01', eYear + '-12'))
# Slice down to Northeast Pacific domain.
ds = ds.sel(lat=slice(25, 62), lon=slice(180, 250))
# Take annual JFM means.
month = ds['time.month']
JFM = (month <= 3)
ds_winter = ds.where(JFM).resample('A', 'time')
# Compute EOF
coslat = np.cos(np.deg2rad(ds_winter.lat.values))
wgts = np.sqrt(coslat)[..., np.newaxis]
solver = Eof(ds_winter, weights=wgts, center=False)
print("NPGO computed.")
eof = solver.eofsAsCorrelation(neofs=2)
variance = solver.varianceFraction(neigs=2)
# Reconstruct the monthly index of SSTa by projecting
# these values onto the annual PC timeseries.
pseudo_pc = solver.projectField(ds, neofs=2, eofscaling=1)
# Set up as dataset.
ds = eof.to_dataset()
ds['pc'] = pseudo_pc
ds['variance_fraction'] = variance
ds = ds.rename({'eofs': 'eof'})
ds = ds.sel(mode=1)
# Invert to the proper values for the bullseye.
if ds.sel(lat=45.5, lon=210).eof < 0:
pass
else:
ds['eof'] = ds['eof'] * -1
ds['pc'] = ds['pc'] * -1
# Change some attributes for the variables.
ds['eof'].attrs['long_name'] = 'Correlation between PC and JFM SSTa'
ds['pc'].attrs['long_name'] = 'Principal component for NPGO'
# Add a description of methods for clarity.
ds.attrs[
'description'] = 'Second mode of JFM SSTa variability over 25-62N and 180-110W.'
ds.attrs[
'anomalies'] = 'Anomalies were computed by removing the ensemble mean at each grid cell.'
ds.attrs['weighting'] = (
'The native grid was regridded to a standard 1deg x 1deg (180x360) grid.'
+ 'Weighting was computed via the sqrt of the cosine of latitude.')
print("Saving to netCDF...")
ds.to_netcdf('/glade/p/work/rbrady/NPGO/NPGO.' + ens + '.' + str(sYear) +
'-' + str(eYear) + '.nc')