def def_sponge_dampingtimescale_north(Y,sponge_width,idampval):
'''Define a sponge grid at the north of the domain based on horizontal grid shape.
hgrid is the horizontal grid dataset
sponge_width is the degrees of lat to damp over [must be a list, progressively decreasing in width]
idampval is the inverse damping rate (in s-1) [must be a list] '''
idamp = xr.zeros_like(Y)
for i in range(len(sponge_width)):
sponge_region = Y>Y.max(xr.ALL_DIMS)-sponge_width[i]
idamp=idamp+xr.zeros_like(Y).where(~sponge_region,idampval[i])
return idamp
def def_sponge_damping_linear_north(Y, sponge_width, idampval_max):
'''Define a sponge grid at the north of the domain based on horizontal grid shape.
hgrid is the horizontal grid dataset
sponge_width is the degrees of lat to damp over and idampval is the inverse damping rate (in s-1)
The function prescribes a linear inverse damping rate and it decays from maximum at the northern boundary
to 0 at end of the sponge width region. '''
idamp = xr.zeros_like(Y)
sponge_region = Y > Y.max(xr.ALL_DIMS) - sponge_width
idamp = idamp + xr.zeros_like(Y).where(~sponge_region, idampval_max)
idamp = idamp * (Y - Y.max(xr.ALL_DIMS) + sponge_width) / sponge_width
return idamp
def reduce_chunked(self, xs, output):
"""Computes the skew across a chunk
Parameters
----------
xs : iterable
Iterable of sources
Returns
-------
UnitsDataArray
Skew of the source data over dims
"""
N = xr.zeros_like(output)
M1 = xr.zeros_like(output)
M2 = xr.zeros_like(output)
M3 = xr.zeros_like(output)
check_empty = True
for x in xs:
Nx = np.isfinite(x).sum(dim=self._dims)
M1x = x.mean(dim=self._dims)
Ex = x - M1x
Ex2 = Ex**2
Ex3 = Ex2 * Ex
M2x = (Ex2).sum(dim=self._dims)
M3x = (Ex3).sum(dim=self._dims)
# premask to omit NaNs
b = Nx.data > 0
Nx = Nx.data[b]
M1x = M1x.data[b]
M2x = M2x.data[b]
M3x = M3x.data[b]
Nb = N.data[b]
M1b = M1.data[b]
M2b = M2.data[b]
# merge
d = M1x - M1b
n = Nb + Nx
NNx = Nb * Nx
M3.data[b] += (M3x + d**3 * NNx * (Nb - Nx) / n**2 + 3 * d *
(Nb * M2x - Nx * M2b) / n)
M2.data[b] += M2x + d**2 * NNx / n
M1.data[b] += d * Nx / n
N.data[b] = n
# calculate skew
skew = np.sqrt(N) * M3 / np.sqrt(M2**3)
return skew
def _invert_from_model_any(inc, sigma0_co_db, sigma0_cr_db, dsig_cr, ancillary_wind):
# wrapper to allow computation on any type (xarray, numpy)
try:
# if input is xarray, will return xarray
da_ws_co = xr.zeros_like(sigma0_co_db, dtype=np.complex128)
da_ws_co.name = 'windspeed_gmf'
da_ws_co.attrs.clear()
da_ws_cr = xr.zeros_like(sigma0_co_db, dtype=np.float64)
da_ws_cr.name = 'windspeed_gmf'
da_ws_cr.attrs.clear()
try:
# if dask array, use map_blocks
# raise ImportError
import dask.array as da
if any(
[
isinstance(v.data, da.Array)
for v in [inc, sigma0_co_db, sigma0_cr_db, dsig_cr, ancillary_wind]
]
):
da_ws_co.data, da_ws_cr.data = da.apply_gufunc(
_invert_from_model_numpy,
'(n),(n),(n),(n),(n)->(n),(n)',
inc.data, sigma0_co_db.data, sigma0_cr_db.data, dsig_cr.data, ancillary_wind.data
)
logger.debug('invert with map_blocks')
else:
raise TypeError
except (ImportError, TypeError):
# use numpy array, but store in xarray
da_ws_co.data, da_ws_cr.data = _invert_from_model_numpy(
np.asarray(inc),
np.asarray(sigma0_co_db),
np.asarray(sigma0_cr_db),
np.asarray(dsig_cr),
np.asarray(ancillary_wind),
)
logger.debug('invert with xarray.values. no chunks')
except TypeError:
# full numpy
logger.debug('invert with numpy')
da_ws_co, da_ws_cr = _invert_from_model_numpy(
inc,
sigma0_co_db,
sigma0_cr_db,
dsig_cr,
ancillary_wind
)
return da_ws_co, da_ws_cr
def main (era_filesearch, cesm_base_filesearch, bias_output):
print("opening data")
era_data = xr.open_mfdataset(era_filesearch, concat_dim='time')
base_cesm_data = xr.open_mfdataset(cesm_base_filesearch, concat_dim='time')
print("loading data")
era_data.load()
base_cesm_data.load()
print("compute means")
emean = era_data.std(dim="time")
cmean = base_cesm_data.std(dim="time")
print("creating data")
interpolated_era = xr.zeros_like(cmean)
print("loading data")
interpolated_era.load()
z_interp_all_vars(emean, interpolated_era, era_data["z"].mean(dim="time"), base_cesm_data["z"].mean(dim="time"), vars_to_correct)
interpolated_era.to_netcdf("era_interpolated_std.nc")
print("Computing Bias")
bias = interpolated_era - cmean
print("writing")
bias.to_netcdf(bias_output)
def construct_knn_graph(
cls,
data,
dist_mat,
k: int,
cell_properties: Union[bool, Sequence[str]] = False,
cell_channel_properties: Union[bool, Sequence[str]] = False
) -> 'SpatialCellGraph':
"""Constructs a new k-nearest cell neighbor graph
:param data: single-cell data (rows: cell IDs, columns: feature names)
:type data: SingleCellData or DataFrame-like
:param dist_mat: symmetric distance matrix, shape: ``(cells, cells)``
:type dist_mat: DataArray-like
:param k: number of nearest neighbors for the graph construction
:param cell_properties: list of cell properties (e.g. regionprops) to include as node attributes; set to
``True`` to include all
:param cell_channel_properties: list of cell channel properties (e.g. intensity values) to include as node
attributes; set to ``True`` to include all
:return: a directed k-nearest cell neighbor graph
"""
data, dist_mat = cls._prepare_data(data, dist_mat, cell_properties,
cell_channel_properties)
adj_mat = xr.zeros_like(dist_mat, dtype='bool')
knn_indices = np.argpartition(dist_mat.values, k + 1,
axis=1)[:, :(k + 1)]
for current_index, current_knn_indices in enumerate(knn_indices):
adj_mat[current_index, current_knn_indices] = True
np.fill_diagonal(adj_mat.values, False)
return SpatialCellGraph(data, adj_mat, _skip_data_preparation=True)
def _regrid_given_delp(
ds,
delp_fine,
delp_coarse,
weights,
x_dim: str = FV_CORE_X_CENTER,
y_dim: str = FV_CORE_Y_CENTER,
z_dim: str = RESTART_Z_CENTER,
):
"""Given a fine and coarse delp, do vertical regridding to coarse pressure levels
and mask weights below fine surface pressure.
"""
delp_coarse_on_fine = block_upsample_like(
delp_coarse, delp_fine, x_dim=x_dim, y_dim=y_dim
)
phalf_coarse_on_fine = pressure_at_interface(
delp_coarse_on_fine, dim_center=z_dim, dim_outer=RESTART_Z_OUTER
)
phalf_fine = pressure_at_interface(
delp_fine, dim_center=z_dim, dim_outer=RESTART_Z_OUTER
)
ds_regrid = xr.zeros_like(ds)
for var in ds:
ds_regrid[var] = regrid_vertical(
phalf_fine, ds[var], phalf_coarse_on_fine, z_dim_center=z_dim
)
masked_weights = _mask_weights(
weights, phalf_coarse_on_fine, phalf_fine, dim_center=z_dim
)
return ds_regrid, masked_weights
def compute_climatology(ds,
monthValues,
calendar=None,
maskVaries=True): # {{{
"""
Compute a monthly, seasonal or annual climatology data set from a data
set. The mean is weighted but the number of days in each month of
the data set, ignoring values masked out with NaNs. If the month
coordinate is not present, a data array ``month`` will be added based
on ``Time`` and the provided calendar.
Parameters
----------
ds : ``xarray.Dataset`` or ``xarray.DataArray`` object
A data set with a ``Time`` coordinate expressed as days since
0001-01-01 or ``month`` coordinate
monthValues : int or array-like of ints
A single month or an array of months to be averaged together
calendar : ``{'gregorian', 'gregorian_noleap'}``, optional
The name of one of the calendars supported by MPAS cores, used to
determine ``month`` from ``Time`` coordinate, so must be supplied if
``ds`` does not already have a ``month`` coordinate or data array
maskVaries: bool, optional
If the mask (where variables in ``ds`` are ``NaN``) varies with time.
If not, the weighted average does not need make extra effort to account
for the mask. Most MPAS fields will have masks that don't vary in
time, whereas observations may sometimes be present only at some
times and not at others, requiring ``maskVaries = True``.
Returns
-------
climatology : object of same type as ``ds``
A data set without the ``'Time'`` coordinate containing the mean
of ds over all months in monthValues, weighted by the number of days
in each month.
Authors
-------
Xylar Asay-Davis
Last Modified
-------------
04/08/2017
"""
ds = add_years_months_days_in_month(ds, calendar)
mask = xr.zeros_like(ds.month, bool)
for month in monthValues:
mask = xr.ufuncs.logical_or(mask, ds.month == month)
climatologyMonths = ds.where(mask, drop=True)
climatology = _compute_masked_mean(climatologyMonths, maskVaries)
return climatology # }}}
def plot(G):
# Don't plot first or last bin (expanded to capture full range)
G = G.isel(sigma0=slice(1, -1))
levs = G["sigma0"].values
# Take annual mean and load
G = G.mean("time").load()
# Get terms in dataset
terms = list(G.data_vars)
fig, ax = plt.subplots()
# Plot each term
for term in terms:
if term == "heat":
color = "tab:red"
elif term == "salt":
color = "tab:blue"
else:
color = "k"
ax.plot(levs, G[term], label=term, color=color)
# If terms were not grouped then sum them up to get total
if len(terms) > 1:
total = xr.zeros_like(G[terms[0]])
for term in terms:
total += G[term]
ax.plot(levs, total, label="total", color="k")
ax.legend()
ax.set_xlabel("SIGMA0")
ax.set_ylabel("TRANSFORMATION ($m^3s^{-1}$)")
ax.autoscale(enable=True, axis="x", tight=True)
return fig
def day_number_to_date_mars_model(ls_in,
calendar_type='none',
units_in='days since 0000-00-0 00:00:00'):
year_values = xar.zeros_like(ls_in)
my_temp = 1
ls_previous = 0.
dodgy_ls_list = []
for i in range(len(ls_in.squeeze().values) - 1):
if ls_in[i] - ls_previous > 0. and ls_in[i + 1] - ls_in[i] > 0.:
year_values[i] = my_temp
elif ls_in[i] - ls_previous < 0. and ls_in[i + 1] - ls_in[i] > 0.:
year_values[i] = my_temp
elif ls_in[i] - ls_previous > 0. and ls_in[i + 1] - ls_in[i] < 0.:
year_values[i] = my_temp
elif ls_in[i] - ls_previous < 0. and ls_in[i + 1] - ls_in[i] < 0.:
dodgy_ls_list.append(i)
my_temp = my_temp + 1
year_values[i] = my_temp
ls_previous = ls_in[i]
year_values[-1] = my_temp
ls_in[dodgy_ls_list] = 0.
dayofyear_values = np.floor(ls_in)
month_values = np.mod(np.ceil((ls_in / 30.) - 0.5) + 3., 12)
cdftime = cdftime_mars(dayofyear_values, month_values, year_values)
return cdftime, ls_in
def test_merge_into_oceandataset():
# da without name
da = od_in.dataset['XC'] * od_in.dataset['YC']
with pytest.raises(ValueError) as e:
od_out = od_in.merge_into_oceandataset(da)
assert str(
e.value
) == "xarray.DataArray doesn't have a name. Set it using da.rename()"
# da different name
da = da.rename('test')
od_out = od_in.merge_into_oceandataset(da)
assert od_out.dataset['test'].equals(da)
# ds
ds = xr.merge([da.rename('test1'), da.rename('test2')])
od_out = od_in.merge_into_oceandataset(ds)
assert set(['test1', 'test2']).issubset(od_out.dataset.variables)
# da
da = xr.zeros_like(od_in.dataset['XC'])
with pytest.warns(UserWarning):
od_out = od_in.merge_into_oceandataset(da)
with pytest.warns(UserWarning):
od_out = od_in.merge_into_oceandataset(da, overwrite=True)
def _column_dq1(ds: xr.Dataset) -> xr.DataArray:
if "net_heating_due_to_machine_learning" in ds:
warnings.warn(
"'net_heating_due_to_machine_learning' is a deprecated variable name. "
"It will not be supported in future versions of fv3net. Use "
"'column_heating_due_to_machine_learning' instead.",
DeprecationWarning,
)
# fix isochoric vs isobaric transition issue
column_dq1 = 716.95 / 1004 * ds.net_heating_due_to_machine_learning
elif "net_heating" in ds:
warnings.warn(
"'net_heating' is a deprecated variable name. "
"It will not be supported in future versions of fv3net. Use "
"'column_heating_due_to_machine_learning' instead.",
DeprecationWarning,
)
# fix isochoric vs isobaric transition issue
column_dq1 = 716.95 / 1004 * ds.net_heating
elif "column_heating_due_to_machine_learning" in ds:
column_dq1 = ds.column_heating_due_to_machine_learning
elif "storage_of_internal_energy_path_due_to_machine_learning" in ds:
column_dq1 = ds.storage_of_internal_energy_path_due_to_machine_learning
else:
# assume given dataset is for a baseline or verification run
column_dq1 = xr.zeros_like(ds.PRATEsfc)
column_dq1.attrs = {
"long_name": "<dQ1> column integrated heating from ML",
"units": "W/m^2",
}
return column_dq1.rename("column_integrated_dQ1")
def test__bin_stats(ds):
from sciapy.level2.binning import _bin_stats
_ds = ds.copy()
_ds["latitude"] = xr.zeros_like(_ds.latitude)
# binning result
avg_aw = _bin_stats(
_ds,
binvar="latitude", tvar="time",
area_weighted=True,
)
avg_nw = _bin_stats(
_ds,
binvar="latitude", tvar="time",
area_weighted=False,
)
xr.testing.assert_allclose(avg_nw, avg_aw)
# non-weighted mean using standard functions
dims = ("latitude", "time")
stacked = "__stacked__"
_ds = _ds.stack(**{stacked: dims})
ds_avg = _ds.mean(dim=stacked)
ds_cnt = _ds.count(dim=stacked)
ds_std = _ds.std(dim=stacked, ddof=1)
ds_std = ds_std.rename({v: v + "_std" for v in ds_std.data_vars})
ds_cnt = ds_cnt.rename({v: v + "_cnt" for v in ds_cnt.data_vars})
avg_ds = xr.merge([ds_avg, ds_std, ds_cnt])
# Re-create the sum of squared weights
_ws = xr.ones_like(_ds.latitude, dtype=float)
_ws /= _ws.sum(dim=stacked)
avg_ds["wsqsum"] = (_ws**2).sum(dim=stacked)
xr.testing.assert_allclose(avg_nw, avg_ds)
def _column_nq1(ds: xr.Dataset) -> xr.DataArray:
if "column_heating_nudge" in ds:
# name for column integrated temperature nudging in nudge-to-obs
column_nq1 = ds.column_heating_nudge
elif "int_t_dt_nudge" in ds:
# name for column-integrated temperature nudging in X-SHiELD runs
column_nq1 = ds.int_t_dt_nudge
elif "net_heating_due_to_nudging" in ds:
# old name for column integrated temperature nudging in nudge-to-fine
warnings.warn(
"'net_heating_due_to_nudging' is a deprecated variable name. "
"It will not be supported in future versions of fv3net. Use "
"'column_heating_due_to_nudging' instead.",
DeprecationWarning,
)
# fix isochoric vs isobaric transition issue
column_nq1 = 716.95 / 1004 * ds.net_heating_due_to_nudging
elif "column_heating_due_to_nudging" in ds:
column_nq1 = ds.column_heating_due_to_nudging
else:
# assume given dataset is for a run without temperature nudging
column_nq1 = xr.zeros_like(ds.PRATEsfc)
column_nq1.attrs = {
"long_name": "<nQ1> column integrated heating from nudging",
"units": "W/m^2",
}
return column_nq1.rename("column_integrated_nQ1")
def wrapper(*args, **kwargs):
fn.utils.assert_isdarray(args[0])
fn.utils.assert_isdarray(args[1])
Ton, Tref = args[:2]
Tout = xr.zeros_like(Ton)
refids = np.unique(Tref.scanid)
onids = np.unique(Ton.scanid)
for onid in tqdm(onids):
# _f denotes former REF (before ON)
# _l denotes latter REF (after ON)
index = np.searchsorted(refids, onid)
if index == 0:
index_f = index_l = 0
elif index == len(refids):
index_f = index_l = len(refids)-1
else:
index_f, index_l = index-1, index
index_on = (Ton.scanid == onid)
index_ref = ((Tref.scanid == refids[index_f])
| (Tref.scanid == refids[index_l]))
Ton_ = Ton[index_on]
Tref_ = Tref[index_ref]
Tout_ = func(Ton_, Tref_, *args[2:], **kwargs)
assert Tout_.shape == Ton_.shape
Tout[index_on] = Tout_
return Tout
def apply_binary_mask(times, dep_lat, dep_lon, mask, reverse=True):
array_list = []
origins = xr.zeros_like(mask)
for i in numba.prange(times.shape[0]):
time = times[i]
dep_lat_, dep_lon_ = dep_lat.sel(time=time).copy(), dep_lon.sel(
time=time).copy()
dep_lat_nan = np.isnan(dep_lat_.values.flatten())
dep_lon_nan = np.isnan(dep_lon_.values.flatten())
assert (dep_lat_nan == dep_lon_nan).all(), "This should not happen!"
dep_lat_no_nan = dep_lat_.values.flatten()[~dep_lat_nan]
dep_lon_no_nan = dep_lon_.values.flatten()[~dep_lon_nan]
points = [x for x in zip(dep_lat_no_nan, dep_lon_no_nan)]
landsea = list()
for point in points:
landsea.append(
mask.sel(latitude=point[0],
longitude=point[1],
method='nearest').values)
origins.sel(latitude=point[0],
longitude=point[1],
method='nearest').values += 1
vals = dep_lat_.values
if reverse:
vals[~np.isnan(vals)] = [0 if x == 1 else 1 for x in landsea
] # switching sea breeze to 1
else:
vals[~np.isnan(vals)] = [x for x in landsea]
array_list.append(vals)
print("Done time {}".format(time))
return array_list, origins
def compute_by_block(dsx):
"""
"""
# determine index key for each chunk
slices = []
for chunks in dsx.chunks:
L = [
0,
] + list(np.cumsum(chunks))
slices.append([slice(a, b) for a, b in (zip(L[:-1], L[1:]))])
indexes = list(product(*slices))
# allocate memory to receive result
if isinstance(dsx, xr.DataArray):
result = xr.zeros_like(dsx).load()
else:
result = np.zeros(dsx.shape)
#evaluate each chunk one at a time
for index in tqdm_notebook(indexes, leave=False):
block = dsx.__getitem__(index).compute()
result.__setitem__(index, block)
return result
def create_area_grid(da, res=0.1):
da_area = xr.zeros_like(da)
da_area.attrs = {'long_name': 'area', 'units': 'ha'}
da_area.name = 'area'
for lat in da_area.lat.values:
da_area.loc[{'lat': lat}] = calc_area(lat, res)
return da_area
def ismatch(dataarray: xr.DataArray,
pattern: Union[Pattern, str],
flags: re.RegexFlag = 0) -> xr.DataArray:
"""Test whether each string in a DataArray matches a regex pattern.
Args:
dataarray: String DataArray to be compared.
pattern: String or compiled regex pattern.
flags: Regex flags to control the matching behavior.
Returns:
Boolean DataArray each value of which is ``True``
where it matches the pattern and ``False`` otherwise.
Raises:
TypeError: Raised if ``dataarray.dtype`` is not string-like.
"""
if not np.issubdtype(dataarray.dtype, np.str_):
raise TypeError("Can only be used for string DataArray.")
pattern = re.compile(pattern, flags)
search = np.vectorize(lambda string: pattern.search(string))
result = xr.zeros_like(dataarray, bool)
result.values = search(dataarray.values).astype(bool)
return result
def process_per_timestep(dset, flexdust_ds,x0,x1,y0,y1, height=None):
dset = dset.sel(lon=slice(x0,x1), lat=slice(y0,y1))
#interpolate flexdust to match flexpart coordinates
flexdust_ds = flexdust_ds.interp({'lon':dset.lon,'lat':dset.lat})
if height == None:
height = dset.height.values
else:
height = height
scale_factor = (1/height)*1000
print('creating output array')
out_data = xr.zeros_like(dset['spec001_mr'])
for i in range(len(out_data.time)):
temp_data = dset['spec001_mr'].isel(time=i)
time_steps = temp_data.time + temp_data.btime
emission_field = flexdust_ds['Emission'].sel(time=time_steps)
out_data[i] = temp_data.values*emission_field.values*scale_factor
print('finish emsfield*sensitvity')
surface_sensitivity = dset['spec001_mr']
iedate_stamp = dset.time[-1]
ibdate_stamp = dset.time[0]
dset.attrs['iedate'] = str(iedate_stamp.dt.strftime('%Y%m%d').values)
dset.attrs['ietime'] = str(iedate_stamp.dt.strftime('%H%M%S').values)
dset.attrs['ibdate'] = str(ibdate_stamp.dt.strftime('%Y%m%d').values)
dset.attrs['ibtime'] = str(ibdate_stamp.dt.strftime('%H%M%S').values)
return dset, out_data, surface_sensitivity
def distance(
self,
direction: str,
x1: LabeledArray,
x2: LabeledArray,
t: LabeledArray,
) -> LabeledArray:
"""Implementation of calculation of physical distances between points
in this coordinate system. This accounts for potential toroidal skew of
lines.
"""
c = np.ceil(x1).astype(int)
f = np.floor(x1).astype(int)
x_s = (self.x_start[c] - self.x_start[f]) * (x1 - f) + self.x_start[f]
x_e = (self.x_end[c] - self.x_end[f]) * (x1 - f) + self.x_end[f]
z_s = (self.z_start[c] - self.z_start[f]) * (x1 - f) + self.z_start[f]
z_e = (self.z_end[c] - self.z_end[f]) * (x1 - f) + self.z_end[f]
y_s = (self.y_start[c] - self.y_start[f]) * (x1 - f) + self.y_start[f]
y_e = (self.y_end[c] - self.y_end[f]) * (x1 - f) + self.y_end[f]
x = x_s + (x_e - x_s) * x2
y = y_s + (y_e - y_s) * x2
z = z_s + (z_e - z_s) * x2
spacings = np.sqrt(
x.diff(direction)**2 + z.diff(direction)**2 + y.diff(direction)**2)
result = zeros_like(x)
result[{direction: slice(1, None)}] = spacings.cumsum(direction)
return result
def load_turbines(decommissioned=True, replace_nan_values="mean"):
"""Load list of all turbines from CSV file. Includes location, capacity,
etc. Missing values are replaced with NaN values.
The file uswtdb_v1_2_20181001.xml contains more information about the fields.
Parameters
----------
decommissioned : bool
if True merge datasets from official CSV with Excel sheet received via e-mail
replace_nan_values : str
use data imputation to set missing values for turbine diameters and hub heights, set to ""
to disable
Returns
-------
xr.DataSet
"""
turbines_dataframe = pd.read_csv(INPUT_DIR / "wind_turbines_usa" /
"uswtdb_v3_0_1_20200514.csv")
# TODO is this really how it is supposed to be done?
turbines_dataframe.index = turbines_dataframe.index.rename("turbines")
turbines = xr.Dataset.from_dataframe(turbines_dataframe)
# Lets not use the turbine on Guam (avoids a huge bounding box for the USA)
neglected_capacity_kw = turbines.sel(
turbines=turbines.xlong >= 0).t_cap.sum()
assert (neglected_capacity_kw == 275
), f"unexpected total capacity filtered: {neglected_capacity_kw}"
turbines = turbines.sel(turbines=turbines.xlong < 0)
turbines = turbines.set_index(turbines="case_id")
turbines["is_decomissioned"] = xr.zeros_like(turbines.p_year,
dtype=np.bool)
if not decommissioned:
return turbines
turbines_decomissioned = pd.read_excel(
INPUT_DIR / "wind_turbines_usa" / "decom_clean_032520.xlsx",
engine="openpyxl",
)
turbines_decomissioned = xr.Dataset(turbines_decomissioned).rename(
dim_0="turbines")
turbines_decomissioned = turbines_decomissioned.set_index(
turbines="case_id")
turbines = xr.merge((turbines, turbines_decomissioned))
turbines["is_decomissioned"] = turbines.decommiss == "yes"
turbines = turbines.drop_vars("decommiss")
if replace_nan_values:
turbines = estimate_missing(turbines, method=replace_nan_values)
turbines = turbines.chunk(CHUNK_SIZE_TURBINES)
return turbines
def estimate_baseline(T_cal, order=1, weight=None):
"""Estimate polynomial baseline of each sample."""
freq = T_cal.ch - T_cal.ch.mean()
n_freq, n_poly = len(freq), order + 1
# make design matrix
X = np.zeros([n_freq, n_poly])
for i in range(n_poly):
poly = freq**i
X[:, i] = poly / np.linalg.norm(poly)
y = T_cal.values.T
# estimate coeffs by solving linear regression problem
if weight is None:
weight = 1.0
model = LinearRegression(fit_intercept=False)
model.fit(X, y, sample_weight=weight)
# estimate baseline
T_base = xr.zeros_like(T_cal) + model.coef_ @ X.T
for i in range(n_poly):
T_base.coords[f"basis_{i}"] = "ch", X[:, i]
T_base.coords[f"coeff_{i}"] = "t", model.coef_[:, i]
return T_base
def get_D_KL_from_xarray(da_P_X_Y, da_P_X, da_P_Y):
"""
base 10 : Mutual information of
I_matrix = xr.apply_ufunc(func_D_KL, P_X_Y, P_X, P_Y)
return I_matrix.sum()
"""
da_log2 = xr.zeros_like(da_P_X_Y)
import itertools
str_dim_x = da_P_X.dims[0]
str_dim_y = da_P_Y.dims[0]
for realiz_id_x, realiz_id_y in itertools.product(
da_P_X_Y[str_dim_x].values, da_P_X_Y[str_dim_y].values):
p_xy = da_P_X_Y.loc[{str_dim_x: realiz_id_x, str_dim_y: realiz_id_y}]
p_x = da_P_X.loc[{str_dim_x: realiz_id_x}]
p_y = da_P_Y.loc[{str_dim_y: realiz_id_y}]
log_p_xy_over_p_x_p_y = ufunc_log_pxy_over_px_py(p_xy, p_x, p_y)
da_log2.loc[{
str_dim_x: realiz_id_x,
str_dim_y: realiz_id_y
}] = log_p_xy_over_p_x_p_y
# da_log2.loc[{str_dim_x:realiz_id_x, str_dim_y:realiz_id_y}] =
# print("da_log2: ", da_log2)
# print("da_P_X_Y: ", da_P_X_Y)
mutual_information = xr.dot(da_P_X_Y, da_log2)
print("mutual_information (", str_dim_x, ", ", str_dim_y, "): ",
mutual_information.values)
return mutual_information
def calc_correlation_field(xda,
mask,
dimlist=['Z', 'YC'],
n_shift=15,
mask_in_betweens=False):
"""calculate the correlation field for each shifted distance
Parameters
----------
xda : xarray.DataArray
The field to compute correlations on, over the 'sample' dimension
mask : xarra.DataArray
True/False inside/outside of domain
dimlist : list of str
denoting dimensions to compute shifted correlations
n_shift : int
number of shifts to do
mask_in_betweens : bool, optional
if True, then if there is a portion of the domain such that for a
particular dimension, there is a gap between two points, ignore all
points with larger correlation length than where the gap occurs
doesn't affect results much
"""
xds = xr.Dataset()
shifty = np.arange(-n_shift, n_shift + 1)
shifty = xr.DataArray(shifty, coords={'shifty': shifty}, dims=('shifty', ))
xds['shifty'] = shifty
for dim in dimlist:
corrfld = f'corr_{dim.lower()}'
template = xda.isel(sample=0).drop('sample')
xds[corrfld] = xr.zeros_like(shifty * template)
x_deviation = (xda - xda.mean('sample')).where(mask)
x_ssr = np.sqrt((x_deviation**2).sum('sample'))
for s in shifty.values:
y_deviation = x_deviation.shift({dim: s})
numerator = (x_deviation * y_deviation).sum('sample')
y_ssr = np.sqrt((y_deviation**2).sum('sample'))
denominator = x_ssr * y_ssr
xds[corrfld].loc[{'shifty': s}] = numerator / denominator
if mask_in_betweens:
for dim in dimlist:
corrfld = f'corr_{dim.lower()}'
for s in shifty.values:
if s < 0:
bigger_than = shifty < s
else:
bigger_than = shifty > s
imnan = np.isnan(xds[corrfld].sel(shifty=s))
xds[corrfld] = xr.where(bigger_than * imnan, np.nan,
xds[corrfld])
return xds
def test_zero_risk_error(self):
participants, incidence_scenarios = (
sim_test_util.participants_and_forecast())
c = sim_test_util.c_to_test_events()
c['incidence_scaler'] = xr.zeros_like(c.incidence_scaler)
with self.assertRaisesRegex(ValueError,
'impossible to account for incidence!'):
sim.control_arm_events(c, participants, incidence_scenarios)
def filter_months(data_array, month_list):
# To define in GeoDataArray !!!!and GeoDS!!!!
if month_list is not None:
condition = xr.zeros_like(data_array.t)
for i in range(len(data_array.t)):
condition[i] = data_array.t[i].values[()].month in util.months_to_number(month_list)
data_array = data_array.where(condition, drop=True)
return data_array
def crop_months(self, new_month_list):
condition = xr.zeros_like(self.data.t)
for i in range(len(self.data.t)):
condition[i] = self.data.t[i].values[()].month in util.months_to_number(new_month_list)
self.data = self.data.where(condition, drop=True)
self.months = new_month_list
print("____ Data cropped to the new month list.")
return self
def strategy(data):
close = data['futures'].sel(field="close")
commodity = data['commodity']
if commodity.isel(time=-1) > commodity.isel(time=-2) and close.isel(
time=-1) > close.isel(time=-20):
return xr.ones_like(close.isel(time=-1))
else:
return xr.zeros_like(close.isel(time=-1))
def gdf_to_model_dataset(model_ds,
gdf,
modelgrid,
name,
gridtype='structured'):
""" create 3 data-arrays from a geodataframe with oppervlaktewater:
- area: with the area of the geodataframe in the cell
- cond: with the conductance based on the area and bweerstand column in gdf
- peil: with the surface water lvl based on the peil column in the gdf
Parameters
----------
model_ds : xr.DataSet
xarray with model data
gdf : geopandas.GeoDataFrame
polygon shapes with surface water.
modelgrid : flopy grid
model grid.
name : str
name of the polygon shapes, name is used to store data arrays in
model_ds
Returns
-------
model_ds : xarray.Dataset
dataset with modelgrid data. Has
"""
area = xr.zeros_like(model_ds['top'])
cond = xr.zeros_like(model_ds['top'])
peil = xr.zeros_like(model_ds['top'])
for i, row in gdf.iterrows():
area_pol = mgrid.polygon_to_area(modelgrid, row['geometry'],
xr.ones_like(model_ds['top']),
gridtype)
cond = xr.where(area_pol > area, area_pol / row['bweerstand'], cond)
peil = xr.where(area_pol > area, row['peil'], peil)
area = xr.where(area_pol > area, area_pol, area)
model_ds_out = util.get_model_ds_empty(model_ds)
model_ds_out[f'{name}_area'] = area
model_ds_out[f'{name}_cond'] = cond
model_ds_out[f'{name}_peil'] = peil
return model_ds_out
def test_binarize():
binarize_spec = Preprocessing(name="binarize", kwargs={"threshold": 14})
data = xr.DataArray(np.arange(30).reshape(2, 3, 5), dims=("x", "y", "c"))
expected = xr.zeros_like(data)
expected[{"x": slice(1, None)}] = 1
preprocessing = make_preprocessing([binarize_spec])
result = preprocessing(data)
xr.testing.assert_allclose(expected, result)
def test_inversion(self):
# Download the RGI file for the run
# Make a new dataframe of those
rgidf = gpd.read_file(get_demo_file('SouthGlacier.shp'))
# Go - initialize working directories
gdirs = workflow.init_glacier_regions(rgidf)
# Preprocessing tasks
task_list = [
tasks.glacier_masks,
tasks.compute_centerlines,
tasks.initialize_flowlines,
tasks.catchment_area,
tasks.catchment_intersections,
tasks.catchment_width_geom,
tasks.catchment_width_correction,
tasks.process_cru_data,
tasks.local_t_star,
tasks.mu_star_calibration,
]
for task in task_list:
execute_entity_task(task, gdirs)
# Inversion tasks
execute_entity_task(tasks.prepare_for_inversion, gdirs)
# We use the default parameters for this run
execute_entity_task(tasks.mass_conservation_inversion, gdirs)
execute_entity_task(tasks.distribute_thickness_per_altitude, gdirs,
varname_suffix='_alt')
execute_entity_task(tasks.distribute_thickness_interp, gdirs,
varname_suffix='_int')
# Reference data
gdir = gdirs[0]
df = self.get_ref_data(gdir)
with xr.open_dataset(gdir.get_filepath('gridded_data')) as ds:
v = ds.distributed_thickness_alt
df['oggm_alt'] = v.isel(x=('z', df['i']), y=('z', df['j']))
v = ds.distributed_thickness_int
df['oggm_int'] = v.isel(x=('z', df['i']), y=('z', df['j']))
ds['ref'] = xr.zeros_like(ds.distributed_thickness_int) * np.NaN
ds['ref'].data[df['j'], df['i']] = df['thick']
rmsd_int = ((df.oggm_int - df.thick) ** 2).mean() ** .5
rmsd_alt = ((df.oggm_int - df.thick) ** 2).mean() ** .5
assert rmsd_int < 80
assert rmsd_alt < 80
dfm = df.mean()
np.testing.assert_allclose(dfm.thick, dfm.oggm_int, 50)
np.testing.assert_allclose(dfm.thick, dfm.oggm_alt, 50)
if do_plot:
import matplotlib.pyplot as plt
df.plot(kind='scatter', x='oggm_int', y='thick')
plt.axis('equal')
df.plot(kind='scatter', x='oggm_alt', y='thick')
plt.axis('equal')
f, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(12, 3))
ds.ref.plot(ax=ax1)
ds.distributed_thickness_int.plot(ax=ax2)
ds.distributed_thickness_alt.plot(ax=ax3)
plt.tight_layout()
plt.show()
def test_optimize_inversion(self):
# Download the RGI file for the run
# Make a new dataframe of those
rgidf = gpd.read_file(get_demo_file('SouthGlacier.shp'))
# Go - initialize working directories
gdirs = workflow.init_glacier_regions(rgidf)
# Preprocessing tasks
task_list = [
tasks.glacier_masks,
tasks.compute_centerlines,
tasks.initialize_flowlines,
tasks.catchment_area,
tasks.catchment_intersections,
tasks.catchment_width_geom,
tasks.catchment_width_correction,
tasks.process_cru_data,
tasks.local_t_star,
tasks.mu_star_calibration,
]
for task in task_list:
execute_entity_task(task, gdirs)
# Reference data
gdir = gdirs[0]
df = self.get_ref_data(gdir)
# Inversion tasks
execute_entity_task(tasks.prepare_for_inversion, gdirs)
glen_a = cfg.PARAMS['inversion_glen_a']
fs = cfg.PARAMS['inversion_fs']
def to_optimize(x):
tasks.mass_conservation_inversion(gdir,
glen_a=glen_a * x[0],
fs=fs * x[1])
tasks.distribute_thickness_per_altitude(gdir)
with xr.open_dataset(gdir.get_filepath('gridded_data')) as ds:
thick = ds.distributed_thickness.isel(x=('z', df['i']),
y=('z', df['j']))
out = (np.abs(thick - df.thick)).mean()
return out
opti = optimization.minimize(to_optimize, [1., 1.],
bounds=((0.01, 10), (0.01, 10)),
tol=0.1)
# Check results and save.
execute_entity_task(tasks.mass_conservation_inversion, gdirs,
glen_a=glen_a*opti['x'][0],
fs=0)
execute_entity_task(tasks.distribute_thickness_per_altitude, gdirs)
with xr.open_dataset(gdir.get_filepath('gridded_data')) as ds:
df['oggm'] = ds.distributed_thickness.isel(x=('z', df['i']),
y=('z', df['j']))
ds['ref'] = xr.zeros_like(ds.distributed_thickness) * np.NaN
ds['ref'].data[df['j'], df['i']] = df['thick']
rmsd = ((df.oggm - df.thick) ** 2).mean() ** .5
assert rmsd < 60
dfm = df.mean()
np.testing.assert_allclose(dfm.thick, dfm.oggm, 10)
if do_plot:
import matplotlib.pyplot as plt
df.plot(kind='scatter', x='oggm', y='thick')
plt.axis('equal')
f, (ax1, ax2) = plt.subplots(1, 2, figsize=(8, 3))
ds.ref.plot(ax=ax1)
ds.distributed_thickness.plot(ax=ax2)
plt.tight_layout()
plt.show()
