def load_dataset(
self, first_date: np.datetime64,
last_date: np.datetime64) -> pyinterp.backends.xarray.Grid3D:
"""Loads the 3D cube describing the SSH in time and space."""
if first_date < self.ts["date"][0] or last_date > self.ts["date"][-1]:
raise IndexError(
f"period [{first_date}, {last_date}] is out of range: "
f"[{self.ts['date'][0]}, {self.ts['date'][-1]}]")
first_date -= self.dt
last_date += self.dt
selected = self.ts["path"][:]
ds = xr.open_mfdataset(selected,
concat_dim="time",
combine="nested",
decode_times=False)
ds = ds.sel(depth=0)
x_axis = pyinterp.Axis(ds.variables["lon"][:], is_circle=True)
y_axis = pyinterp.Axis(ds.variables["lat"][:])
hours = (ds.variables['time'][:].data *
3600000000).astype('timedelta64[us]')
time = np.datetime64('2000') + hours
z_axis = pyinterp.TemporalAxis(time)
var = ds.surf_el[:].T
return pyinterp.Grid3D(x_axis, y_axis, z_axis, var)
def test_bicubic():
grid = pyinterp.backends.xarray.Grid2D(xr.load_dataset(GRID).mss)
lon = np.arange(-180, 180, 1) + 1 / 3.0
lat = np.arange(-90, 90, 1) + 1 / 3.0
x, y = np.meshgrid(lon, lat, indexing="ij")
z = grid.bicubic(collections.OrderedDict(lon=x.flatten(), lat=y.flatten()))
assert isinstance(z, np.ndarray)
for fitting_model in [
'linear', 'bicubic', 'polynomial', 'c_spline', 'c_spline_periodic',
'akima', 'akima_periodic', 'steffen'
]:
other = grid.bicubic(collections.OrderedDict(lon=x.flatten(),
lat=y.flatten()),
fitting_model=fitting_model)
assert (z - other).mean() != 0
with pytest.raises(ValueError):
grid.bicubic(collections.OrderedDict(lon=x.flatten(), lat=y.flatten()),
bounds_error=True)
with pytest.raises(ValueError):
grid.bicubic(collections.OrderedDict(lon=x.flatten(), lat=y.flatten()),
bounds_error=True,
boundary="sym")
x_axis = pyinterp.Axis(np.linspace(-180, 179, 360), is_circle=True)
y_axis = pyinterp.Axis(np.linspace(-90, 90, 181), is_circle=False)
z_axis = pyinterp.Axis(np.linspace(0, 10, 10), is_circle=False)
matrix, _ = np.meshgrid(x_axis[:], y_axis[:])
grid = pyinterp.Grid2D(x_axis, y_axis, matrix.T)
assert isinstance(grid, pyinterp.Grid2D)
with pytest.raises(ValueError):
pyinterp.bicubic(grid, x.flatten(), y.flatten(), fitting_model='_')
with pytest.raises(ValueError):
pyinterp.bicubic(grid, x.flatten(), y.flatten(), boundary='_')
grid = pyinterp.Grid2D(x_axis.flip(inplace=False), y_axis, matrix.T)
with pytest.raises(ValueError):
pyinterp.bicubic(grid, x.flatten(), y.flatten())
grid = pyinterp.Grid2D(x_axis, y_axis.flip(), matrix.T)
with pytest.raises(ValueError):
pyinterp.bicubic(grid, x.flatten(), y.flatten())
matrix, _, _ = np.meshgrid(x_axis[:], y_axis[:], z_axis[:])
grid = pyinterp.Grid3D(x_axis, y_axis, z_axis, matrix.transpose(1, 0, 2))
with pytest.raises(ValueError):
pyinterp.bicubic(grid, x.flatten(), y.flatten())
grid = pyinterp.backends.xarray.RegularGridInterpolator(
xr.load_dataset(GRID).mss)
assert grid.ndim == 2
assert isinstance(grid.grid, pyinterp.backends.xarray.Grid2D)
z = grid(collections.OrderedDict(lon=x.flatten(), lat=y.flatten()),
method="bicubic",
bicubic_kwargs=dict(nx=3, ny=3))
assert isinstance(z, np.ndarray)
def bfn_grid_dataset(list_of_file, var2add, var2sub,
lon_min=0., lon_max=360.,
lat_min=-90, lat_max=90.,
time_min='1900-10-01', time_max='2100-01-01', is_circle=True):
ds = xr.open_mfdataset(list_of_file, concat_dim ='time', combine='nested', parallel=True)
ds = ds.sel(time=slice(time_min, time_max))
ds = ds.where((ds["lon"]%360. >= lon_min) & (ds["lon"]%360. <= lon_max), drop=True)
ds = ds.where((ds["lat"] >= lat_min) & (ds["lat"] <= lat_max), drop=True)
x_axis = pyinterp.Axis(ds["lon"][:]%360., is_circle=is_circle)
y_axis = pyinterp.Axis(ds["lat"][:])
z_axis = pyinterp.TemporalAxis(ds["time"][:])
for variable_name in var2add:
try:
var += ds[variable_name][:]
except UnboundLocalError:
var = ds[variable_name][:]
for variable_name in var2sub:
try:
var -= ds[variable_name][:]
except UnboundLocalError:
var = ds[variable_name][:]
# MB clean boundary for file OSE_GULFSTREAM_FPGENN.nc
#var.values[:, 0:3, :] = np.nan
#var.values[:, :, 0:3] = np.nan
# ds['time'] = (ds['time'] - np.datetime64('1950-01-01T00:00:00Z')) / np.timedelta64(1, 'D')
var = var.transpose('lon', 'lat', 'time')
# The undefined values must be set to nan.
try:
var[var.mask] = float("nan")
except AttributeError:
pass
grid = pyinterp.Grid3D(x_axis, y_axis, z_axis, var.data)
del ds
return x_axis, y_axis, z_axis, grid
def dymost_grid_dataset(list_of_file, var2add, var2sub,
lon_min=0., lon_max=360.,
lat_min=-90, lat_max=90.,
time_min='1900-10-01', time_max='2100-01-01', is_circle=True):
ds = xr.open_mfdataset(list_of_file, concat_dim ='time', combine='nested', parallel=True)
ds = ds.sel(time=slice(time_min, time_max))
ds = ds.where((ds["lon"] >= lon_min) & (ds["lon"] <= lon_max), drop=True)
ds = ds.where((ds["lat"] >= lat_min) & (ds["lat"] <= lat_max), drop=True)
# print(ds)
x_axis = pyinterp.Axis(ds["lon"][0, :], is_circle=is_circle)
y_axis = pyinterp.Axis(ds["lat"][:, 0])
z_axis = pyinterp.TemporalAxis(ds["time"][:])
for variable_name in var2add:
try:
var += ds[variable_name][:] #ds['Ha'][:]
except UnboundLocalError:
var = ds[variable_name][:]
for variable_name in var2sub:
try:
var -= ds[variable_name][:]
except UnboundLocalError:
var = ds[variable_name][:]
var = var.transpose('x', 'y', 'time')
# The undefined values must be set to nan.
try:
var[var.mask] = float("nan")
except AttributeError:
pass
grid = pyinterp.Grid3D(x_axis, y_axis, z_axis, var.data)
del ds
return x_axis, y_axis, z_axis, grid
def duacs_grid_dataset(list_of_file, variable_name='Grid_0001',
lon_min=0., lon_max=360.,
lat_min=-90, lat_max=90.,
time_min='1900-10-01', time_max='2100-01-01', is_circle=True):
def preprocess_duacs_maps(ds):
vtime = ds[variable_name].attrs['Date_CNES_JD']
ds.coords['time'] = np.datetime64(netCDF4.num2date(vtime, units='days since 1950-01-01'))
if ds[variable_name].units == 'cm':
ds[variable_name] = ds[variable_name] / 100.
ds[variable_name].attrs = {'units': 'm'}
return ds
ds = xr.open_mfdataset(list_of_file, concat_dim ='time', combine='nested', parallel=True, preprocess=preprocess_duacs_maps)
ds = ds.sel(time=slice(time_min, time_max))
ds = ds.where((ds["NbLongitudes"] >= lon_min) & (ds["NbLongitudes"] <= lon_max), drop=True)
ds = ds.where((ds["NbLatitudes"] >= lat_min) & (ds["NbLatitudes"] <= lat_max), drop=True)
x_axis = pyinterp.Axis(ds["NbLongitudes"][:], is_circle=is_circle)
y_axis = pyinterp.Axis(ds["NbLatitudes"][:])
z_axis = pyinterp.TemporalAxis(ds["time"][:])
var = ds[variable_name][:].transpose('NbLongitudes', 'NbLatitudes', 'time')
# The undefined values must be set to nan.
try:
var[var.mask] = float("nan")
except AttributeError:
pass
grid = pyinterp.Grid3D(x_axis, y_axis, z_axis, var.data)
del ds
return x_axis, y_axis, z_axis, grid
def read_l4_dataset(list_of_file,
lon_min=0.,
lon_max=360.,
lat_min=-90,
lat_max=90.,
time_min='1900-10-01',
time_max='2100-01-01',
is_circle=True):
ds = xr.open_mfdataset(list_of_file,
concat_dim='time',
combine='nested',
parallel=True)
ds = ds.sel(time=slice(time_min, time_max), drop=True)
ds = ds.where(
(ds["lon"] % 360. >= lon_min) & (ds["lon"] % 360. <= lon_max),
drop=True)
ds = ds.where((ds["lat"] >= lat_min) & (ds["lat"] <= lat_max), drop=True)
x_axis = pyinterp.Axis(ds["lon"][:] % 360., is_circle=is_circle)
y_axis = pyinterp.Axis(ds["lat"][:])
z_axis = pyinterp.TemporalAxis(ds["time"][:])
var = ds['ssh'][:]
var = var.transpose('lon', 'lat', 'time')
# The undefined values must be set to nan.
try:
var[var.mask] = float("nan")
except AttributeError:
pass
grid = pyinterp.Grid3D(x_axis, y_axis, z_axis, var.data)
del ds
return x_axis, y_axis, z_axis, grid
def oi_regrid(ds_source, ds_target):
logging.info(' Regridding...')
# Define source grid
x_source_axis = pyinterp.Axis(ds_source["lon"][:], is_circle=False)
y_source_axis = pyinterp.Axis(ds_source["lat"][:])
z_source_axis = pyinterp.TemporalAxis(ds_source["time"][:])
ssh_source = ds_source["gssh"][:].T
grid_source = pyinterp.Grid3D(x_source_axis, y_source_axis, z_source_axis,
ssh_source.data)
# Define target grid
mx_target, my_target, mz_target = numpy.meshgrid(
ds_target['lon'].values,
ds_target['lat'].values,
z_source_axis.safe_cast(ds_target['time'].values),
indexing="ij")
# Spatio-temporal Interpolation
ssh_interp = pyinterp.trivariate(grid_source,
mx_target.flatten(),
my_target.flatten(),
mz_target.flatten(),
bounds_error=True).reshape(
mx_target.shape).T
# Save to dataset
ds_ssh_interp = xr.Dataset(
{'sossheig': (('time', 'lat', 'lon'), ssh_interp)},
coords={
'time': ds_target['time'].values,
'lon': ds_target['lon'].values,
'lat': ds_target['lat'].values,
})
return ds_ssh_interp
def load_dataset(
self, first_date: np.datetime64,
last_date: np.datetime64) -> pyinterp.backends.xarray.Grid3D:
"""Loads the 3D cube describing the SSH in time and space."""
if first_date < self.ts["date"][0] or last_date > self.ts["date"][-1]:
raise IndexError(
f"period [{first_date}, {last_date}] is out of range: "
f"[{self.ts['date'][0]}, {self.ts['date'][-1]}]")
first_date -= self.dt
last_date += self.dt
selected = self.ts["path"][(self.ts["date"] >= first_date)
& (self.ts["date"] < last_date)]
ds = xr.open_mfdataset(selected,
concat_dim="time",
combine="nested",
decode_times=True)
x_axis = pyinterp.Axis(ds.variables["longitude"][:], is_circle=True)
y_axis = pyinterp.Axis(ds.variables["latitude"][:])
z_axis = pyinterp.TemporalAxis(ds.time)
var = ds.wlv[:].T
return pyinterp.Grid3D(x_axis, y_axis, z_axis, var)
def interpolate(self, lon: np.ndarray, lat: np.ndarray,
dates: np.ndarray) -> np.ndarray:
"""Interpolate the SSH to the required coordinates."""
ds = self._select_ds(
dates.min(), # type: ignore
dates.max()) # type: ignore
assert np.all(np.diff(ds.ocean_time.values) == self._dt)
assert np.all(np.diff(ds.lon_rho.values, axis=0) < 1e-10)
assert np.all(np.diff(ds.lat_rho.values, axis=1) < 1e-10)
t_axis = pyinterp.TemporalAxis(ds.ocean_time.values)
grid3d = pyinterp.Grid3D(
pyinterp.Axis(ds.lon_rho.values[0, :], is_circle=True),
pyinterp.Axis(ds.lat_rho.values[:, 0]), t_axis,
ds[self.ssh].values.T)
ssh = pyinterp.trivariate(grid3d,
lon.ravel(),
lat.ravel(),
t_axis.safe_cast(dates.ravel()),
num_threads=1).reshape(lon.shape)
return ssh
# tensor data so that it is properly stored in memory for pyinterp.
#%%
# * The shape of the tensor must be (len(x_axis), len(y_axis), len(t_axis))
tcw = tcw.T
#%%
# * The undefined values must be set to nan.
tcw[tcw.mask] = float("nan")
#%%
# Now we can build the object handling the regular 3-dimensional grid.
#
# .. note::
# Grid data are not copied, the Grid3D class just keeps a reference on the
# handled array. Axis data are copied for non-uniform axes, and only examined
# for regular axes.
grid_3d = pyinterp.Grid3D(x_axis, y_axis, t_axis, tcw)
grid_3d
#%%
# xarray backend
# ##############
#
# The construction of these objects manipulating the :py:class:`regular grids
# <pyinterp.backends.xarray.RegularGridInterpolator>` can be done more easily
# using the `xarray <http://xarray.pydata.org/>`_ library and `CF
# <https://cfconventions.org/>`_ convention usually found in NetCDF files.
interpolator = pyinterp.backends.xarray.RegularGridInterpolator(
xarray.open_dataset(TCW).tcw)
interpolator.grid