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from __future__ import annotations
from collections import Counter, defaultdict
from collections.abc import Callable, Hashable, Iterable, Iterator, Sequence
from typing import TYPE_CHECKING, Literal, TypeVar, Union, cast
import pandas as pd
from xarray.core import dtypes
from xarray.core.dataarray import DataArray
from xarray.core.dataset import Dataset
from xarray.core.utils import iterate_nested
from xarray.structure.alignment import AlignmentError
from xarray.structure.concat import concat
from xarray.structure.merge import merge
from xarray.util.deprecation_helpers import (
_COMPAT_DEFAULT,
_COORDS_DEFAULT,
_DATA_VARS_DEFAULT,
_JOIN_DEFAULT,
CombineKwargDefault,
)
if TYPE_CHECKING:
from xarray.core.types import (
CombineAttrsOptions,
CompatOptions,
JoinOptions,
NestedSequence,
)
T = TypeVar("T")
def _infer_concat_order_from_positions(
datasets: NestedSequence[T],
) -> dict[tuple[int, ...], T]:
return dict(_infer_tile_ids_from_nested_list(datasets, ()))
def _infer_tile_ids_from_nested_list(
entry: NestedSequence[T], current_pos: tuple[int, ...]
) -> Iterator[tuple[tuple[int, ...], T]]:
"""
Given a list of lists (of lists...) of objects, returns a iterator
which returns a tuple containing the index of each object in the nested
list structure as the key, and the object. This can then be called by the
dict constructor to create a dictionary of the objects organised by their
position in the original nested list.
Recursively traverses the given structure, while keeping track of the
current position. Should work for any type of object which isn't a list.
Parameters
----------
entry : list[list[obj, obj, ...], ...]
List of lists of arbitrary depth, containing objects in the order
they are to be concatenated.
Returns
-------
combined_tile_ids : dict[tuple(int, ...), obj]
"""
if not isinstance(entry, str) and isinstance(entry, Sequence):
for i, item in enumerate(entry):
yield from _infer_tile_ids_from_nested_list(item, current_pos + (i,))
else:
yield current_pos, cast(T, entry)
def _ensure_same_types(series, dim):
if series.dtype == object:
types = set(series.map(type))
if len(types) > 1:
try:
import cftime
cftimes = any(issubclass(t, cftime.datetime) for t in types)
except ImportError:
cftimes = False
types = ", ".join(t.__name__ for t in types)
error_msg = (
f"Cannot combine along dimension '{dim}' with mixed types."
f" Found: {types}."
)
if cftimes:
error_msg = (
f"{error_msg} If importing data directly from a file then "
f"setting `use_cftime=True` may fix this issue."
)
raise TypeError(error_msg)
def _infer_concat_order_from_coords(datasets):
concat_dims = []
tile_ids = [() for ds in datasets]
# All datasets have same variables because they've been grouped as such
ds0 = datasets[0]
for dim in ds0.dims:
# Check if dim is a coordinate dimension
if dim in ds0:
# Need to read coordinate values to do ordering
indexes = [ds._indexes.get(dim) for ds in datasets]
if any(index is None for index in indexes):
error_msg = (
f"Every dimension requires a corresponding 1D coordinate "
f"and index for inferring concatenation order but the "
f"coordinate '{dim}' has no corresponding index"
)
raise ValueError(error_msg)
# TODO (benbovy, flexible indexes): support flexible indexes?
indexes = [index.to_pandas_index() for index in indexes]
# If dimension coordinate values are same on every dataset then
# should be leaving this dimension alone (it's just a "bystander")
if not all(index.equals(indexes[0]) for index in indexes[1:]):
# Infer order datasets should be arranged in along this dim
concat_dims.append(dim)
if all(index.is_monotonic_increasing for index in indexes):
ascending = True
elif all(index.is_monotonic_decreasing for index in indexes):
ascending = False
else:
raise ValueError(
f"Coordinate variable {dim} is neither "
"monotonically increasing nor "
"monotonically decreasing on all datasets"
)
# Assume that any two datasets whose coord along dim starts
# with the same value have the same coord values throughout.
if any(index.size == 0 for index in indexes):
raise ValueError("Cannot handle size zero dimensions")
first_items = pd.Index([index[0] for index in indexes])
series = first_items.to_series()
# ensure series does not contain mixed types, e.g. cftime calendars
_ensure_same_types(series, dim)
# Sort datasets along dim
# We want rank but with identical elements given identical
# position indices - they should be concatenated along another
# dimension, not along this one
rank = series.rank(
method="dense", ascending=ascending, numeric_only=False
)
order = rank.astype(int).values - 1
# Append positions along extra dimension to structure which
# encodes the multi-dimensional concatenation order
tile_ids = [
tile_id + (position,)
for tile_id, position in zip(tile_ids, order, strict=True)
]
if len(datasets) > 1 and not concat_dims:
raise ValueError(
"Could not find any dimension coordinates to use to "
"order the datasets for concatenation"
)
combined_ids = dict(zip(tile_ids, datasets, strict=True))
return combined_ids, concat_dims
def _check_dimension_depth_tile_ids(combined_tile_ids):
"""
Check all tuples are the same length, i.e. check that all lists are
nested to the same depth.
"""
tile_ids = combined_tile_ids.keys()
nesting_depths = [len(tile_id) for tile_id in tile_ids]
if not nesting_depths:
nesting_depths = [0]
if set(nesting_depths) != {nesting_depths[0]}:
raise ValueError(
"The supplied objects do not form a hypercube because"
" sub-lists do not have consistent depths"
)
# return these just to be reused in _check_shape_tile_ids
return tile_ids, nesting_depths
def _check_shape_tile_ids(combined_tile_ids):
"""Check all lists along one dimension are same length."""
tile_ids, nesting_depths = _check_dimension_depth_tile_ids(combined_tile_ids)
for dim in range(nesting_depths[0]):
indices_along_dim = [tile_id[dim] for tile_id in tile_ids]
occurrences = Counter(indices_along_dim)
if len(set(occurrences.values())) != 1:
raise ValueError(
"The supplied objects do not form a hypercube "
"because sub-lists do not have consistent "
f"lengths along dimension {dim}"
)
def _combine_nd(
combined_ids,
concat_dims,
data_vars,
coords,
compat: CompatOptions | CombineKwargDefault,
fill_value,
join: JoinOptions | CombineKwargDefault,
combine_attrs: CombineAttrsOptions,
):
"""
Combines an N-dimensional structure of datasets into one by applying a
series of either concat and merge operations along each dimension.
No checks are performed on the consistency of the datasets, concat_dims or
tile_IDs, because it is assumed that this has already been done.
Parameters
----------
combined_ids : Dict[Tuple[int, ...]], xarray.Dataset]
Structure containing all datasets to be concatenated with "tile_IDs" as
keys, which specify position within the desired final combined result.
concat_dims : sequence of str
The dimensions along which the datasets should be concatenated. Must be
in order, and the length must match the length of the tuples used as
keys in combined_ids. If the string is a dimension name then concat
along that dimension, if it is None then merge.
Returns
-------
combined_ds : xarray.Dataset
"""
example_tile_id = next(iter(combined_ids.keys()))
n_dims = len(example_tile_id)
if len(concat_dims) != n_dims:
raise ValueError(
f"concat_dims has length {len(concat_dims)} but the datasets "
f"passed are nested in a {n_dims}-dimensional structure"
)
# Each iteration of this loop reduces the length of the tile_ids tuples
# by one. It always combines along the first dimension, removing the first
# element of the tuple
for concat_dim in concat_dims:
combined_ids = _combine_all_along_first_dim(
combined_ids,
dim=concat_dim,
data_vars=data_vars,
coords=coords,
compat=compat,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
(combined_ds,) = combined_ids.values()
return combined_ds
def _combine_all_along_first_dim(
combined_ids,
dim,
data_vars,
coords,
compat: CompatOptions | CombineKwargDefault,
fill_value,
join: JoinOptions | CombineKwargDefault,
combine_attrs: CombineAttrsOptions,
):
# Group into lines of datasets which must be combined along dim
grouped = groupby_defaultdict(list(combined_ids.items()), key=_new_tile_id)
# Combine all of these datasets along dim
new_combined_ids = {}
for new_id, group in grouped:
combined_ids = dict(sorted(group))
datasets = combined_ids.values()
new_combined_ids[new_id] = _combine_1d(
datasets,
concat_dim=dim,
compat=compat,
data_vars=data_vars,
coords=coords,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
return new_combined_ids
def _combine_1d(
datasets,
concat_dim,
compat: CompatOptions | CombineKwargDefault,
data_vars,
coords,
fill_value,
join: JoinOptions | CombineKwargDefault,
combine_attrs: CombineAttrsOptions,
):
"""
Applies either concat or merge to 1D list of datasets depending on value
of concat_dim
"""
if concat_dim is not None:
try:
combined = concat(
datasets,
dim=concat_dim,
data_vars=data_vars,
coords=coords,
compat=compat,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
except ValueError as err:
if "encountered unexpected variable" in str(err):
raise ValueError(
"These objects cannot be combined using only "
"xarray.combine_nested, instead either use "
"xarray.combine_by_coords, or do it manually "
"with xarray.concat, xarray.merge and "
"xarray.align"
) from err
else:
raise
else:
try:
combined = merge(
datasets,
compat=compat,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
except AlignmentError as e:
e.add_note(
"If you are intending to concatenate datasets, please specify the concatenation dimension explicitly. "
"Using merge to concatenate is quite inefficient."
)
raise e
return combined
def _new_tile_id(single_id_ds_pair):
tile_id, ds = single_id_ds_pair
return tile_id[1:]
def _nested_combine(
datasets,
concat_dims,
compat,
data_vars,
coords,
ids,
fill_value,
join: JoinOptions | CombineKwargDefault,
combine_attrs: CombineAttrsOptions,
):
if len(datasets) == 0:
return Dataset()
# Arrange datasets for concatenation
# Use information from the shape of the user input
if not ids:
# Determine tile_IDs by structure of input in N-D
# (i.e. ordering in list-of-lists)
combined_ids = _infer_concat_order_from_positions(datasets)
else:
# Already sorted so just use the ids already passed
combined_ids = dict(zip(ids, datasets, strict=True))
# Check that the inferred shape is combinable
_check_shape_tile_ids(combined_ids)
# Apply series of concatenate or merge operations along each dimension
combined = _combine_nd(
combined_ids,
concat_dims=concat_dims,
compat=compat,
data_vars=data_vars,
coords=coords,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
return combined
# Define type for arbitrarily-nested list of lists recursively:
DATASET_HYPERCUBE = Union[Dataset, Iterable["DATASET_HYPERCUBE"]]
def combine_nested(
datasets: DATASET_HYPERCUBE,
concat_dim: str | DataArray | Sequence[str | DataArray | pd.Index | None],
compat: str | CombineKwargDefault = _COMPAT_DEFAULT,
data_vars: str | CombineKwargDefault = _DATA_VARS_DEFAULT,
coords: str | CombineKwargDefault = _COORDS_DEFAULT,
fill_value: object = dtypes.NA,
join: JoinOptions | CombineKwargDefault = _JOIN_DEFAULT,
combine_attrs: CombineAttrsOptions = "drop",
) -> Dataset:
"""
Explicitly combine an N-dimensional grid of datasets into one by using a
succession of concat and merge operations along each dimension of the grid.
Does not sort the supplied datasets under any circumstances, so the
datasets must be passed in the order you wish them to be concatenated. It
does align coordinates, but different variables on datasets can cause it to
fail under some scenarios. In complex cases, you may need to clean up your
data and use concat/merge explicitly.
To concatenate along multiple dimensions the datasets must be passed as a
nested list-of-lists, with a depth equal to the length of ``concat_dims``.
``combine_nested`` will concatenate along the top-level list first.
Useful for combining datasets from a set of nested directories, or for
collecting the output of a simulation parallelized along multiple
dimensions.
Parameters
----------
datasets : list or nested list of Dataset
Dataset objects to combine.
If concatenation or merging along more than one dimension is desired,
then datasets must be supplied in a nested list-of-lists.
concat_dim : str, or list of str, DataArray, Index or None
Dimensions along which to concatenate variables, as used by
:py:func:`xarray.concat`.
Set ``concat_dim=[..., None, ...]`` explicitly to disable concatenation
and merge instead along a particular dimension.
The position of ``None`` in the list specifies the dimension of the
nested-list input along which to merge.
Must be the same length as the depth of the list passed to
``datasets``.
compat : {"identical", "equals", "broadcast_equals", \
"no_conflicts", "override"}, optional
String indicating how to compare variables of the same name for
potential merge conflicts:
- "broadcast_equals": all values must be equal when variables are
broadcast against each other to ensure common dimensions.
- "equals": all values and dimensions must be the same.
- "identical": all values, dimensions and attributes must be the
same.
- "no_conflicts": only values which are not null in both datasets
must be equal. The returned dataset then contains the combination
of all non-null values.
- "override": skip comparing and pick variable from first dataset
data_vars : {"minimal", "different", "all" or list of str}, optional
These data variables will be concatenated together:
* "minimal": Only data variables in which the dimension already
appears are included.
* "different": Data variables which are not equal (ignoring
attributes) across all datasets are also concatenated (as well as
all for which dimension already appears). Beware: this option may
load the data payload of data variables into memory if they are not
already loaded.
* "all": All data variables will be concatenated.
* None: Means ``"all"`` if ``dim`` is not present in any of the ``objs``,
and ``"minimal"`` if ``dim`` is present in any of ``objs``.
* list of dims: The listed data variables will be concatenated, in
addition to the "minimal" data variables.
coords : {"minimal", "different", "all" or list of str}, optional
These coordinate variables will be concatenated together:
* "minimal": Only coordinates in which the dimension already appears
are included. If concatenating over a dimension _not_
present in any of the objects, then all data variables will
be concatenated along that new dimension.
* "different": Coordinates which are not equal (ignoring attributes)
across all datasets are also concatenated (as well as all for which
dimension already appears). Beware: this option may load the data
payload of coordinate variables into memory if they are not already
loaded.
* "all": All coordinate variables will be concatenated, except
those corresponding to other dimensions.
* list of Hashable: The listed coordinate variables will be concatenated,
in addition to the "minimal" coordinates.
fill_value : scalar or dict-like, optional
Value to use for newly missing values. If a dict-like, maps
variable names to fill values. Use a data array's name to
refer to its values.
join : {"outer", "inner", "left", "right", "exact"}, optional
String indicating how to combine differing indexes
(excluding concat_dim) in objects
- "outer": use the union of object indexes
- "inner": use the intersection of object indexes
- "left": use indexes from the first object with each dimension
- "right": use indexes from the last object with each dimension
- "exact": instead of aligning, raise `ValueError` when indexes to be
aligned are not equal
- "override": if indexes are of same size, rewrite indexes to be
those of the first object with that dimension. Indexes for the same
dimension must have the same size in all objects.
combine_attrs : {"drop", "identical", "no_conflicts", "drop_conflicts", \
"override"} or callable, default: "drop"
A callable or a string indicating how to combine attrs of the objects being
merged:
- "drop": empty attrs on returned Dataset.
- "identical": all attrs must be the same on every object.
- "no_conflicts": attrs from all objects are combined, any that have
the same name must also have the same value.
- "drop_conflicts": attrs from all objects are combined, any that have
the same name but different values are dropped.
- "override": skip comparing and copy attrs from the first dataset to
the result.
If a callable, it must expect a sequence of ``attrs`` dicts and a context object
as its only parameters.
Returns
-------
combined : xarray.Dataset
Examples
--------
A common task is collecting data from a parallelized simulation in which
each process wrote out to a separate file. A domain which was decomposed
into 4 parts, 2 each along both the x and y axes, requires organising the
datasets into a doubly-nested list, e.g:
>>> x1y1 = xr.Dataset(
... {
... "temperature": (("x", "y"), np.random.randn(2, 2)),
... "precipitation": (("x", "y"), np.random.randn(2, 2)),
... }
... )
>>> x1y1
<xarray.Dataset> Size: 64B
Dimensions: (x: 2, y: 2)
Dimensions without coordinates: x, y
Data variables:
temperature (x, y) float64 32B 1.764 0.4002 0.9787 2.241
precipitation (x, y) float64 32B 1.868 -0.9773 0.9501 -0.1514
>>> x1y2 = xr.Dataset(
... {
... "temperature": (("x", "y"), np.random.randn(2, 2)),
... "precipitation": (("x", "y"), np.random.randn(2, 2)),
... }
... )
>>> x2y1 = xr.Dataset(
... {
... "temperature": (("x", "y"), np.random.randn(2, 2)),
... "precipitation": (("x", "y"), np.random.randn(2, 2)),
... }
... )
>>> x2y2 = xr.Dataset(
... {
... "temperature": (("x", "y"), np.random.randn(2, 2)),
... "precipitation": (("x", "y"), np.random.randn(2, 2)),
... }
... )
>>> ds_grid = [[x1y1, x1y2], [x2y1, x2y2]]
>>> combined = xr.combine_nested(ds_grid, concat_dim=["x", "y"])
>>> combined
<xarray.Dataset> Size: 256B
Dimensions: (x: 4, y: 4)
Dimensions without coordinates: x, y
Data variables:
temperature (x, y) float64 128B 1.764 0.4002 -0.1032 ... 0.04576 -0.1872
precipitation (x, y) float64 128B 1.868 -0.9773 0.761 ... 0.1549 0.3782
``combine_nested`` can also be used to explicitly merge datasets with
different variables. For example if we have 4 datasets, which are divided
along two times, and contain two different variables, we can pass ``None``
to ``concat_dim`` to specify the dimension of the nested list over which
we wish to use ``merge`` instead of ``concat``:
>>> t1temp = xr.Dataset({"temperature": ("t", np.random.randn(5))})
>>> t1temp
<xarray.Dataset> Size: 40B
Dimensions: (t: 5)
Dimensions without coordinates: t
Data variables:
temperature (t) float64 40B -0.8878 -1.981 -0.3479 0.1563 1.23
>>> t1precip = xr.Dataset({"precipitation": ("t", np.random.randn(5))})
>>> t1precip
<xarray.Dataset> Size: 40B
Dimensions: (t: 5)
Dimensions without coordinates: t
Data variables:
precipitation (t) float64 40B 1.202 -0.3873 -0.3023 -1.049 -1.42
>>> t2temp = xr.Dataset({"temperature": ("t", np.random.randn(5))})
>>> t2precip = xr.Dataset({"precipitation": ("t", np.random.randn(5))})
>>> ds_grid = [[t1temp, t1precip], [t2temp, t2precip]]
>>> combined = xr.combine_nested(ds_grid, concat_dim=["t", None])
>>> combined
<xarray.Dataset> Size: 160B
Dimensions: (t: 10)
Dimensions without coordinates: t
Data variables:
temperature (t) float64 80B -0.8878 -1.981 -0.3479 ... -0.4381 -1.253
precipitation (t) float64 80B 1.202 -0.3873 -0.3023 ... -0.8955 0.3869
See also
--------
concat
merge
"""
mixed_datasets_and_arrays = any(
isinstance(obj, Dataset) for obj in iterate_nested(datasets)
) and any(
isinstance(obj, DataArray) and obj.name is None
for obj in iterate_nested(datasets)
)
if mixed_datasets_and_arrays:
raise ValueError("Can't combine datasets with unnamed arrays.")
if isinstance(concat_dim, str | DataArray) or concat_dim is None:
concat_dim = [concat_dim]
# The IDs argument tells _nested_combine that datasets aren't yet sorted
return _nested_combine(
datasets,
concat_dims=concat_dim,
compat=compat,
data_vars=data_vars,
coords=coords,
ids=False,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
def vars_as_keys(ds):
return tuple(sorted(ds))
K = TypeVar("K", bound=Hashable)
def groupby_defaultdict(
iter: list[T],
key: Callable[[T], K],
) -> Iterator[tuple[K, Iterator[T]]]:
"""replacement for itertools.groupby"""
idx = defaultdict(list)
for i, obj in enumerate(iter):
idx[key(obj)].append(i)
for k, ix in idx.items():
yield k, (iter[i] for i in ix)
def _combine_single_variable_hypercube(
datasets,
fill_value,
data_vars,
coords,
compat: CompatOptions | CombineKwargDefault,
join: JoinOptions | CombineKwargDefault,
combine_attrs: CombineAttrsOptions,
):
"""
Attempt to combine a list of Datasets into a hypercube using their
coordinates.
All provided Datasets must belong to a single variable, ie. must be
assigned the same variable name. This precondition is not checked by this
function, so the caller is assumed to know what it's doing.
This function is NOT part of the public API.
"""
if len(datasets) == 0:
raise ValueError(
"At least one Dataset is required to resolve variable names "
"for combined hypercube."
)
combined_ids, concat_dims = _infer_concat_order_from_coords(list(datasets))
if fill_value is None:
# check that datasets form complete hypercube
_check_shape_tile_ids(combined_ids)
else:
# check only that all datasets have same dimension depth for these
# vars
_check_dimension_depth_tile_ids(combined_ids)
# Concatenate along all of concat_dims one by one to create single ds
concatenated = _combine_nd(
combined_ids,
concat_dims=concat_dims,
data_vars=data_vars,
coords=coords,
compat=compat,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
# Check the overall coordinates are monotonically increasing
for dim in concat_dims:
indexes = concatenated.indexes.get(dim)
if not (indexes.is_monotonic_increasing or indexes.is_monotonic_decreasing):
raise ValueError(
"Resulting object does not have monotonic"
f" global indexes along dimension {dim}"
)
return concatenated
def combine_by_coords(
data_objects: Iterable[Dataset | DataArray] = [],
compat: CompatOptions | CombineKwargDefault = _COMPAT_DEFAULT,
data_vars: Literal["all", "minimal", "different"]
| None
| list[str]
| CombineKwargDefault = _DATA_VARS_DEFAULT,
coords: str | CombineKwargDefault = _COORDS_DEFAULT,
fill_value: object = dtypes.NA,
join: JoinOptions | CombineKwargDefault = _JOIN_DEFAULT,
combine_attrs: CombineAttrsOptions = "no_conflicts",
) -> Dataset | DataArray:
"""
Attempt to auto-magically combine the given datasets (or data arrays)
into one by using dimension coordinates.
This function attempts to combine a group of datasets along any number of
dimensions into a single entity by inspecting coords and metadata and using
a combination of concat and merge.
Will attempt to order the datasets such that the values in their dimension
coordinates are monotonic along all dimensions. If it cannot determine the
order in which to concatenate the datasets, it will raise a ValueError.
Non-coordinate dimensions will be ignored, as will any coordinate
dimensions which do not vary between each dataset.
Aligns coordinates, but different variables on datasets can cause it
to fail under some scenarios. In complex cases, you may need to clean up
your data and use concat/merge explicitly (also see `combine_nested`).
Works well if, for example, you have N years of data and M data variables,
and each combination of a distinct time period and set of data variables is
saved as its own dataset. Also useful for if you have a simulation which is
parallelized in multiple dimensions, but has global coordinates saved in
each file specifying the positions of points within the global domain.
Parameters
----------
data_objects : Iterable of Datasets or DataArrays
Data objects to combine.
compat : {"identical", "equals", "broadcast_equals", "no_conflicts", "override"}, optional
String indicating how to compare variables of the same name for
potential conflicts:
- "broadcast_equals": all values must be equal when variables are
broadcast against each other to ensure common dimensions.
- "equals": all values and dimensions must be the same.
- "identical": all values, dimensions and attributes must be the
same.
- "no_conflicts": only values which are not null in both datasets
must be equal. The returned dataset then contains the combination
of all non-null values.
- "override": skip comparing and pick variable from first dataset
data_vars : {"minimal", "different", "all" or list of str}, optional
These data variables will be concatenated together:
- "minimal": Only data variables in which the dimension already
appears are included.
- "different": Data variables which are not equal (ignoring
attributes) across all datasets are also concatenated (as well as
all for which dimension already appears). Beware: this option may
load the data payload of data variables into memory if they are not
already loaded.
- "all": All data variables will be concatenated.
- list of str: The listed data variables will be concatenated, in
addition to the "minimal" data variables.
If objects are DataArrays, `data_vars` must be "all".
coords : {"minimal", "different", "all"} or list of str, optional
As per the "data_vars" kwarg, but for coordinate variables.
fill_value : scalar or dict-like, optional
Value to use for newly missing values. If a dict-like, maps
variable names to fill values. Use a data array's name to
refer to its values. If None, raises a ValueError if
the passed Datasets do not create a complete hypercube.
join : {"outer", "inner", "left", "right", "exact"}, optional
String indicating how to combine differing indexes in objects
- "outer": use the union of object indexes
- "inner": use the intersection of object indexes
- "left": use indexes from the first object with each dimension
- "right": use indexes from the last object with each dimension
- "exact": instead of aligning, raise `ValueError` when indexes to be
aligned are not equal
- "override": if indexes are of same size, rewrite indexes to be
those of the first object with that dimension. Indexes for the same
dimension must have the same size in all objects.
combine_attrs : {"drop", "identical", "no_conflicts", "drop_conflicts", \
"override"} or callable, default: "no_conflicts"
A callable or a string indicating how to combine attrs of the objects being
merged:
- "drop": empty attrs on returned Dataset.
- "identical": all attrs must be the same on every object.
- "no_conflicts": attrs from all objects are combined, any that have
the same name must also have the same value.
- "drop_conflicts": attrs from all objects are combined, any that have
the same name but different values are dropped.
- "override": skip comparing and copy attrs from the first dataset to
the result.
If a callable, it must expect a sequence of ``attrs`` dicts and a context object
as its only parameters.
Returns
-------
combined : xarray.Dataset or xarray.DataArray
Will return a Dataset unless all the inputs are unnamed DataArrays, in which case a
DataArray will be returned.
See also
--------
concat
merge
combine_nested
Examples
--------
Combining two datasets using their common dimension coordinates. Notice
they are concatenated based on the values in their dimension coordinates,
not on their position in the list passed to `combine_by_coords`.
>>> x1 = xr.Dataset(
... {
... "temperature": (("y", "x"), 20 * np.random.rand(6).reshape(2, 3)),
... "precipitation": (("y", "x"), np.random.rand(6).reshape(2, 3)),
... },
... coords={"y": [0, 1], "x": [10, 20, 30]},
... )
>>> x2 = xr.Dataset(
... {
... "temperature": (("y", "x"), 20 * np.random.rand(6).reshape(2, 3)),
... "precipitation": (("y", "x"), np.random.rand(6).reshape(2, 3)),
... },
... coords={"y": [2, 3], "x": [10, 20, 30]},
... )
>>> x3 = xr.Dataset(
... {
... "temperature": (("y", "x"), 20 * np.random.rand(6).reshape(2, 3)),
... "precipitation": (("y", "x"), np.random.rand(6).reshape(2, 3)),
... },
... coords={"y": [2, 3], "x": [40, 50, 60]},
... )
>>> x1
<xarray.Dataset> Size: 136B
Dimensions: (y: 2, x: 3)
Coordinates:
* y (y) int64 16B 0 1
* x (x) int64 24B 10 20 30
Data variables:
temperature (y, x) float64 48B 10.98 14.3 12.06 10.9 8.473 12.92
precipitation (y, x) float64 48B 0.4376 0.8918 0.9637 0.3834 0.7917 0.5289
>>> x2
<xarray.Dataset> Size: 136B
Dimensions: (y: 2, x: 3)
Coordinates:
* y (y) int64 16B 2 3
* x (x) int64 24B 10 20 30
Data variables:
temperature (y, x) float64 48B 11.36 18.51 1.421 1.743 0.4044 16.65
precipitation (y, x) float64 48B 0.7782 0.87 0.9786 0.7992 0.4615 0.7805
>>> x3
<xarray.Dataset> Size: 136B
Dimensions: (y: 2, x: 3)
Coordinates:
* y (y) int64 16B 2 3
* x (x) int64 24B 40 50 60
Data variables:
temperature (y, x) float64 48B 2.365 12.8 2.867 18.89 10.44 8.293
precipitation (y, x) float64 48B 0.2646 0.7742 0.4562 0.5684 0.01879 0.6176
>>> xr.combine_by_coords([x2, x1])
<xarray.Dataset> Size: 248B
Dimensions: (y: 4, x: 3)
Coordinates:
* y (y) int64 32B 0 1 2 3
* x (x) int64 24B 10 20 30
Data variables:
temperature (y, x) float64 96B 10.98 14.3 12.06 ... 1.743 0.4044 16.65
precipitation (y, x) float64 96B 0.4376 0.8918 0.9637 ... 0.4615 0.7805
>>> xr.combine_by_coords([x3, x1], join="outer")
<xarray.Dataset> Size: 464B
Dimensions: (y: 4, x: 6)
Coordinates:
* y (y) int64 32B 0 1 2 3
* x (x) int64 48B 10 20 30 40 50 60
Data variables:
temperature (y, x) float64 192B 10.98 14.3 12.06 ... 18.89 10.44 8.293
precipitation (y, x) float64 192B 0.4376 0.8918 0.9637 ... 0.01879 0.6176
>>> xr.combine_by_coords([x3, x1], join="override")
<xarray.Dataset> Size: 256B
Dimensions: (y: 2, x: 6)
Coordinates:
* y (y) int64 16B 0 1
* x (x) int64 48B 10 20 30 40 50 60
Data variables:
temperature (y, x) float64 96B 10.98 14.3 12.06 ... 18.89 10.44 8.293
precipitation (y, x) float64 96B 0.4376 0.8918 0.9637 ... 0.01879 0.6176
>>> xr.combine_by_coords([x1, x2, x3], join="outer")
<xarray.Dataset> Size: 464B
Dimensions: (y: 4, x: 6)
Coordinates:
* y (y) int64 32B 0 1 2 3
* x (x) int64 48B 10 20 30 40 50 60
Data variables:
temperature (y, x) float64 192B 10.98 14.3 12.06 ... 18.89 10.44 8.293
precipitation (y, x) float64 192B 0.4376 0.8918 0.9637 ... 0.01879 0.6176
You can also combine DataArray objects, but the behaviour will differ depending on
whether or not the DataArrays are named. If all DataArrays are named then they will
be promoted to Datasets before combining, and then the resultant Dataset will be
returned, e.g.
>>> named_da1 = xr.DataArray(
... name="a", data=[1.0, 2.0], coords={"x": [0, 1]}, dims="x"
... )
>>> named_da1
<xarray.DataArray 'a' (x: 2)> Size: 16B
array([1., 2.])
Coordinates:
* x (x) int64 16B 0 1
>>> named_da2 = xr.DataArray(
... name="a", data=[3.0, 4.0], coords={"x": [2, 3]}, dims="x"
... )
>>> named_da2
<xarray.DataArray 'a' (x: 2)> Size: 16B
array([3., 4.])
Coordinates:
* x (x) int64 16B 2 3
>>> xr.combine_by_coords([named_da1, named_da2])
<xarray.Dataset> Size: 64B
Dimensions: (x: 4)
Coordinates:
* x (x) int64 32B 0 1 2 3
Data variables:
a (x) float64 32B 1.0 2.0 3.0 4.0
If all the DataArrays are unnamed, a single DataArray will be returned, e.g.
>>> unnamed_da1 = xr.DataArray(data=[1.0, 2.0], coords={"x": [0, 1]}, dims="x")
>>> unnamed_da2 = xr.DataArray(data=[3.0, 4.0], coords={"x": [2, 3]}, dims="x")
>>> xr.combine_by_coords([unnamed_da1, unnamed_da2])
<xarray.DataArray (x: 4)> Size: 32B
array([1., 2., 3., 4.])
Coordinates:
* x (x) int64 32B 0 1 2 3
Finally, if you attempt to combine a mix of unnamed DataArrays with either named
DataArrays or Datasets, a ValueError will be raised (as this is an ambiguous operation).
"""
if not data_objects:
return Dataset()
objs_are_unnamed_dataarrays = [
isinstance(data_object, DataArray) and data_object.name is None
for data_object in data_objects
]
if any(objs_are_unnamed_dataarrays):
if all(objs_are_unnamed_dataarrays):
# Combine into a single larger DataArray
temp_datasets = [
unnamed_dataarray._to_temp_dataset()
for unnamed_dataarray in data_objects
]
combined_temp_dataset = _combine_single_variable_hypercube(
temp_datasets,
fill_value=fill_value,
data_vars=data_vars,
coords=coords,
compat=compat,
join=join,
combine_attrs=combine_attrs,
)
return DataArray()._from_temp_dataset(combined_temp_dataset)
else:
# Must be a mix of unnamed dataarrays with either named dataarrays or with datasets
# Can't combine these as we wouldn't know whether to merge or concatenate the arrays
raise ValueError(
"Can't automatically combine unnamed DataArrays with either named DataArrays or Datasets."
)
else:
# Promote any named DataArrays to single-variable Datasets to simplify combining
data_objects = [
obj.to_dataset() if isinstance(obj, DataArray) else obj
for obj in data_objects
]
# Group by data vars
grouped_by_vars = groupby_defaultdict(data_objects, key=vars_as_keys)
# Perform the multidimensional combine on each group of data variables
# before merging back together
concatenated_grouped_by_data_vars = tuple(
_combine_single_variable_hypercube(
tuple(datasets_with_same_vars),
fill_value=fill_value,
data_vars=data_vars,
coords=coords,
compat=compat,
join=join,
combine_attrs=combine_attrs,
)
for vars, datasets_with_same_vars in grouped_by_vars
)
return merge(
concatenated_grouped_by_data_vars,
compat=compat,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
|