#!/usr/bin/env python
# Copyright (c) 2022, openradar developers.
# Distributed under the MIT License. See LICENSE for more info.
"""
CfRadial1
=========
This sub-module contains the CfRadial1 xarray backend for reading CfRadial1-based radar
data into Xarray structures as well as a reader to create a complete datatree.Datatree.
Code ported from wradlib.
Example::
import xradar as xd
dtree = xd.io.open_cfradial1_datatree(filename)
.. autosummary::
:nosignatures:
:toctree: generated/
{}
"""
__all__ = [
"CfRadial1BackendEntrypoint",
"open_cfradial1_datatree",
]
__doc__ = __doc__.format("\n ".join(__all__))
import numpy as np
from datatree import DataTree
from xarray import open_dataset
from xarray.backends import NetCDF4DataStore
from xarray.backends.common import BackendEntrypoint
from xarray.backends.store import StoreBackendEntrypoint
from ... import util
from ...model import (
conform_cfradial2_sweep_group,
georeferencing_correction_subgroup,
optional_root_attrs,
optional_root_vars,
radar_calibration_subgroup,
radar_parameters_subgroup,
required_global_attrs,
required_root_vars,
)
from .common import _attach_sweep_groups, _maybe_decode
def _get_required_root_dataset(ds, optional=True):
"""Extract Root Dataset."""
# keep only defined mandatory and defined optional variables per default
var = ds.variables.keys()
remove_root = set(var) ^ set(required_root_vars)
if optional:
remove_root ^= set(optional_root_vars)
remove_root ^= {"sweep_number", "fixed_angle"}
remove_root &= var
root = ds.drop_vars(remove_root)
# rename variables
# todo: find a more easy method not iterating over all variables
for k in root.data_vars:
rename = optional_root_vars.get(k, None)
if rename:
root = root.rename_vars({k: rename})
# keep only defined mandatory and defined optional attributes per default
attrs = root.attrs.keys()
remove_attrs = set(attrs) ^ set(required_global_attrs)
if optional:
remove_attrs ^= set(optional_root_attrs)
for k in remove_attrs:
root.attrs.pop(k, None)
# handle sweep variables and dimension
root = root.rename_vars(
{"sweep_number": "sweep_group_name", "fixed_angle": "sweep_fixed_angle"}
)
root["sweep_group_name"].values = np.array(
[f"sweep_{i}" for i in root["sweep_group_name"].values]
)
# fix dtype in encoding
root.sweep_group_name.encoding["dtype"] = root.sweep_group_name.dtype
# remove cf standard name
root.sweep_group_name.attrs = []
return root
def _get_sweep_groups(
obj, sweep=None, first_dim="auto", optional=True, site_coords=True
):
"""Extract Sweep Groups.
Parameters
----------
obj : xarray.Dataset
CfRadial1 Dataset
Keyword Arguments
-----------------
sweep : str, int, optional
Sweep/Group to extract, default to None.
first_dim : str
Can be ``time`` or ``auto`` first dimension. If set to ``auto``,
first dimension will be either ``azimuth`` or ``elevation`` depending on
type of sweep. Defaults to ``auto``.
optional : bool
Import optional mandatory data and metadata, defaults to ``True``.
site_coords : bool
Attach radar site-coordinates to Dataset, defaults to ``True``.
Ported from wradlib.
"""
# get hold of sweep start/stop indices and remove variables
start_idx = obj.sweep_start_ray_index.values.astype(int)
end_idx = obj.sweep_end_ray_index.values.astype(int)
root = obj.drop_vars(["sweep_start_ray_index", "sweep_end_ray_index"])
ray_n_gates = root.get("ray_n_gates", False)
ray_start_index = root.get("ray_start_index", False)
# strip variables and attributes
anc_dims = list(set(root.dims) ^ {"time", "range", "sweep"})
root = root.drop_dims(anc_dims)
root = root.rename({"fixed_angle": "sweep_fixed_angle"})
# conform to cfradial2 standard
data = conform_cfradial2_sweep_group(root, optional, "time")
# which sweeps to load
# sweep is assumed a list of strings with elements like "sweep_0"
sweep_groups = {}
if isinstance(sweep, str):
sweep = [sweep]
elif isinstance(sweep, int):
sweep = [f"sweep_{sweep}"]
# iterate over sweeps
for i in range(root.sizes["sweep"]):
sw = f"sweep_{i}"
if sweep is not None and not (sw in sweep or i in sweep):
continue
# slice time and sweep dimension
tslice = slice(start_idx[i], end_idx[i] + 1)
swslice = slice(i, i + 1)
ds = data.isel(time=tslice, sweep=swslice).squeeze("sweep")
ds["sweep_mode"] = _maybe_decode(ds.sweep_mode).compute()
dim0 = "elevation" if ds["sweep_mode"] == "rhi" else "azimuth"
# check and extract for variable number of gates
if ray_n_gates is not False:
# swap dimensions to correctly stack/unstack n_points = ["time", "range"]
ds = ds.swap_dims({"time": dim0})
current_ray_n_gates = ray_n_gates.isel(time=tslice)
current_rays_sum = current_ray_n_gates.sum().values.astype(int)
nslice = slice(
ray_start_index[start_idx[i]].values.astype(int),
ray_start_index[start_idx[i]].values.astype(int) + current_rays_sum,
)
rslice = slice(0, current_ray_n_gates[0].values.astype(int))
ds = ds.isel(range=rslice)
ds = ds.isel(n_points=nslice)
ds = ds.stack(n_points=[dim0, "range"])
ds = ds.unstack("n_points")
# fix elevation/time additional range dimension in coordinate
ds = ds.assign_coords({"elevation": ds.elevation.isel(range=0, drop=True)})
# handling first dimension
# for CfRadial1 first dimension is time
if first_dim == "auto":
ds = ds.swap_dims({"time": dim0})
ds = ds.sortby(dim0)
# reassign azimuth/elevation coordinates
ds = ds.assign_coords({"azimuth": ds.azimuth})
ds = ds.assign_coords({"elevation": ds.elevation})
# assign site_coords
if site_coords:
ds = ds.assign_coords(
{
"latitude": root.latitude,
"longitude": root.longitude,
"altitude": root.altitude,
}
)
sweep_groups[sw] = ds
return sweep_groups
def _get_cfradial2_group(
ds, sweep="sweep_0", first_dim="time", optional=True, site_coords=False
):
"""Assign CfRadial2 group from CfRadial1 data structure.
Parameters
----------
ds : xarray.Dataset
Dataset of CfRadial1 file
sweep : str, int, optional
Sweep/Group to extract, default to first sweep.
first_dim : str
Can be ``time`` or ``auto`` first dimension. If set to ``auto``,
first dimension will be either ``azimuth`` or ``elevation`` depending on
type of sweep. Defaults to ``auto``.
optional : bool
Import optional mandatory data and metadata, defaults to ``True``.
site_coords : bool
Attach radar site-coordinates to Dataset, defaults to ``True``.
Returns
-------
sweep : xarray.Dataset
CfRadial2 group.
"""
if sweep in ["/", "root"]:
return _get_required_root_dataset(ds, optional=optional)
elif sweep in ["radar_calibration", "calib", "r_calib"]:
return _get_radar_calibration(ds)
elif sweep in ["radar_parameters"]:
return _get_subgroup(ds, radar_parameters_subgroup)
elif sweep in ["georeferencing_correction"]:
return _get_subgroup(ds, georeferencing_correction_subgroup)
elif "sweep" in sweep:
return list(
_get_sweep_groups(
ds,
sweep,
first_dim=first_dim,
optional=optional,
site_coords=site_coords,
).values()
)[0]
else:
return None
def _get_subgroup(ds, subdict):
"""Get CfRadial2 root metadata group.
Variables are fetched from the provided Dataset according to the subdict dictionary.
"""
meta_vars = subdict
extract_vars = set(ds.data_vars) & set(meta_vars)
subgroup = ds[extract_vars]
for k in subgroup.data_vars:
rename = meta_vars[k]
if rename:
subgroup = subgroup.rename_vars({k: rename})
subgroup.attrs = {}
return subgroup
def _get_radar_calibration(ds):
"""Get radar calibration root metadata group."""
# radar_calibration is connected with calib-dimension
calib = [anc for anc in ds.dims if "calib" in anc]
if calib:
# extract group variables
subgroup = ds.drop_dims(list(set(ds.dims) ^ {calib[0]}))
drop = [k for k, v in subgroup.variables.items() if calib[0] not in v.dims]
subgroup = subgroup.drop_vars(drop).squeeze(calib[0])
calib_vars = {}
for name in subgroup.data_vars:
item = next(
filter(lambda x: x[0] in name, radar_calibration_subgroup.items())
)
item = item[1] if item[1] else item[0]
calib_vars[name] = item
subgroup = subgroup.rename_vars(calib_vars)
subgroup.attrs = {}
return subgroup
[docs]
def open_cfradial1_datatree(filename_or_obj, **kwargs):
"""Open CfRadial1 dataset as :py:class:`datatree.DataTree`.
Parameters
----------
filename_or_obj : str, Path, file-like or xarray.DataStore
Strings and Path objects are interpreted as a path to a local or remote
radar file
Keyword Arguments
-----------------
sweep : int, list of int, optional
Sweep number(s) to extract, default to first sweep. If None, all sweeps are
extracted into a list.
first_dim : str
Can be ``time`` or ``auto`` first dimension. If set to ``auto``,
first dimension will be either ``azimuth`` or ``elevation`` depending on
type of sweep. Defaults to ``auto``.
reindex_angle : bool or dict
Defaults to False, no reindexing. Given dict should contain the kwargs to
reindex_angle. Only invoked if `decode_coord=True`.
fix_second_angle : bool
If True, fixes erroneous second angle data. Defaults to ``False``.
optional : bool
Import optional mandatory data and metadata, defaults to ``True``.
site_coords : bool
Attach radar site-coordinates to Dataset, defaults to ``True``.
Returns
-------
dtree: datatree.DataTree
DataTree with CfRadial2 groups.
"""
# handle kwargs, extract first_dim
first_dim = kwargs.pop("first_dim", "auto")
optional = kwargs.pop("optional", True)
site_coords = kwargs.pop("site_coords", True)
sweep = kwargs.pop("sweep", None)
# open root group, cfradial1 only has one group
# open_cfradial1_datatree only opens the file once using netcdf4
# and retrieves the different groups from the loaded object
ds = open_dataset(filename_or_obj, engine="netcdf4", **kwargs)
# create datatree root node with required data
root = _get_required_root_dataset(ds, optional=optional)
dtree = DataTree(data=root, name="root")
# additional root metadata groups
# radar_parameters
subgroup = _get_subgroup(ds, radar_parameters_subgroup)
DataTree(subgroup, name="radar_parameters", parent=dtree)
# radar_calibration (connected with calib-dimension)
calib = _get_radar_calibration(ds)
if calib:
DataTree(calib, name="radar_calibration", parent=dtree)
# georeferencing_correction
subgroup = _get_subgroup(ds, georeferencing_correction_subgroup)
DataTree(subgroup, name="georeferencing_correction", parent=dtree)
# return datatree with attached sweep child nodes
dtree = _attach_sweep_groups(
dtree,
list(
_get_sweep_groups(
ds,
sweep=sweep,
first_dim=first_dim,
optional=optional,
site_coords=site_coords,
).values()
),
)
return dtree
[docs]
class CfRadial1BackendEntrypoint(BackendEntrypoint):
"""Xarray BackendEntrypoint for CfRadial1 data.
Keyword Arguments
-----------------
first_dim : str
Can be ``time`` or ``auto`` first dimension. If set to ``auto``,
first dimension will be either ``azimuth`` or ``elevation`` depending on
type of sweep. Defaults to ``auto``.
reindex_angle : bool or dict
Defaults to False, no reindexing. Given dict should contain the kwargs to
reindex_angle. Only invoked if `decode_coord=True`.
fix_second_angle : bool
For PPI only. If True, fixes erroneous second angle data. Defaults to False.
site_coords : bool
Attach radar site-coordinates to Dataset, defaults to ``True``.
kwargs : dict
Additional kwargs are fed to :py:func:`xarray.open_dataset`.
"""
description = "Open CfRadial1 (.nc, .nc4) using netCDF4 in Xarray"
url = "https://xradar.rtfd.io/en/latest/io.html#cfradial1"
def open_dataset(
self,
filename_or_obj,
*,
mask_and_scale=True,
decode_times=True,
concat_characters=True,
decode_coords=True,
drop_variables=None,
use_cftime=None,
decode_timedelta=None,
format=None,
group="/",
first_dim="auto",
reindex_angle=False,
fix_second_angle=False,
site_coords=True,
optional=True,
):
store = NetCDF4DataStore.open(
filename_or_obj,
format=format,
group=None,
)
store_entrypoint = StoreBackendEntrypoint()
ds0 = store_entrypoint.open_dataset(
store,
mask_and_scale=mask_and_scale,
decode_times=decode_times,
concat_characters=concat_characters,
decode_coords=decode_coords,
drop_variables=drop_variables,
use_cftime=use_cftime,
decode_timedelta=decode_timedelta,
)
ds = _get_cfradial2_group(
ds0,
sweep=group,
first_dim=first_dim,
optional=optional,
site_coords=site_coords,
)
if ds is None:
raise ValueError(f"Group `{group}` missing from file `{filename_or_obj}`.")
if decode_coords and reindex_angle is not False:
ds = ds.pipe(util.remove_duplicate_rays)
ds = ds.pipe(util.reindex_angle, **reindex_angle)
ds = ds.pipe(util.ipol_time, **reindex_angle)
return ds
