from __future__ import annotations
from collections.abc import Hashable, Iterable
from typing import TYPE_CHECKING, Any, Union, overload
import numpy as np
import pandas as pd
from xarray.core import dtypes, utils
from xarray.core.alignment import align, reindex_variables
from xarray.core.duck_array_ops import lazy_array_equiv
from xarray.core.indexes import Index, PandasIndex
from xarray.core.merge import (
_VALID_COMPAT,
collect_variables_and_indexes,
merge_attrs,
merge_collected,
)
from xarray.core.types import T_DataArray, T_Dataset, T_Variable
from xarray.core.variable import Variable
from xarray.core.variable import concat as concat_vars
if TYPE_CHECKING:
from xarray.core.types import (
CombineAttrsOptions,
CompatOptions,
ConcatOptions,
JoinOptions,
)
T_DataVars = Union[ConcatOptions, Iterable[Hashable]]
@overload
def concat(
objs: Iterable[T_Dataset],
dim: Hashable | T_Variable | T_DataArray | pd.Index,
data_vars: T_DataVars = "all",
coords: ConcatOptions | list[Hashable] = "different",
compat: CompatOptions = "equals",
positions: Iterable[Iterable[int]] | None = None,
fill_value: object = dtypes.NA,
join: JoinOptions = "outer",
combine_attrs: CombineAttrsOptions = "override",
) -> T_Dataset: ...
@overload
def concat(
objs: Iterable[T_DataArray],
dim: Hashable | T_Variable | T_DataArray | pd.Index,
data_vars: T_DataVars = "all",
coords: ConcatOptions | list[Hashable] = "different",
compat: CompatOptions = "equals",
positions: Iterable[Iterable[int]] | None = None,
fill_value: object = dtypes.NA,
join: JoinOptions = "outer",
combine_attrs: CombineAttrsOptions = "override",
) -> T_DataArray: ...
[docs]
def concat(
objs,
dim,
data_vars: T_DataVars = "all",
coords="different",
compat: CompatOptions = "equals",
positions=None,
fill_value=dtypes.NA,
join: JoinOptions = "outer",
combine_attrs: CombineAttrsOptions = "override",
):
"""Concatenate xarray objects along a new or existing dimension.
Parameters
----------
objs : sequence of Dataset and DataArray
xarray objects to concatenate together. Each object is expected to
consist of variables and coordinates with matching shapes except for
along the concatenated dimension.
dim : Hashable or Variable or DataArray or pandas.Index
Name of the dimension to concatenate along. This can either be a new
dimension name, in which case it is added along axis=0, or an existing
dimension name, in which case the location of the dimension is
unchanged. If dimension is provided as a Variable, DataArray or Index, its name
is used as the dimension to concatenate along and the values are added
as a coordinate.
data_vars : {"minimal", "different", "all"} or list of Hashable, 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 dims: 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 Hashable, optional
These coordinate variables will be concatenated together:
* "minimal": Only coordinates in which the dimension already appears
are included.
* "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.
compat : {"identical", "equals", "broadcast_equals", "no_conflicts", "override"}, optional
String indicating how to compare non-concatenated variables of the same name for
potential conflicts. This is passed down to merge.
- "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
positions : None or list of integer arrays, optional
List of integer arrays which specifies the integer positions to which
to assign each dataset along the concatenated dimension. If not
supplied, objects are concatenated in the provided order.
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 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: "override"
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
-------
concatenated : type of objs
See also
--------
merge
Examples
--------
>>> da = xr.DataArray(
... np.arange(6).reshape(2, 3), [("x", ["a", "b"]), ("y", [10, 20, 30])]
... )
>>> da
<xarray.DataArray (x: 2, y: 3)> Size: 48B
array([[0, 1, 2],
[3, 4, 5]])
Coordinates:
* x (x) <U1 8B 'a' 'b'
* y (y) int64 24B 10 20 30
>>> xr.concat([da.isel(y=slice(0, 1)), da.isel(y=slice(1, None))], dim="y")
<xarray.DataArray (x: 2, y: 3)> Size: 48B
array([[0, 1, 2],
[3, 4, 5]])
Coordinates:
* x (x) <U1 8B 'a' 'b'
* y (y) int64 24B 10 20 30
>>> xr.concat([da.isel(x=0), da.isel(x=1)], "x")
<xarray.DataArray (x: 2, y: 3)> Size: 48B
array([[0, 1, 2],
[3, 4, 5]])
Coordinates:
* x (x) <U1 8B 'a' 'b'
* y (y) int64 24B 10 20 30
>>> xr.concat([da.isel(x=0), da.isel(x=1)], "new_dim")
<xarray.DataArray (new_dim: 2, y: 3)> Size: 48B
array([[0, 1, 2],
[3, 4, 5]])
Coordinates:
x (new_dim) <U1 8B 'a' 'b'
* y (y) int64 24B 10 20 30
Dimensions without coordinates: new_dim
>>> xr.concat([da.isel(x=0), da.isel(x=1)], pd.Index([-90, -100], name="new_dim"))
<xarray.DataArray (new_dim: 2, y: 3)> Size: 48B
array([[0, 1, 2],
[3, 4, 5]])
Coordinates:
x (new_dim) <U1 8B 'a' 'b'
* y (y) int64 24B 10 20 30
* new_dim (new_dim) int64 16B -90 -100
"""
# TODO: add ignore_index arguments copied from pandas.concat
# TODO: support concatenating scalar coordinates even if the concatenated
# dimension already exists
from xarray.core.dataarray import DataArray
from xarray.core.dataset import Dataset
try:
first_obj, objs = utils.peek_at(objs)
except StopIteration:
raise ValueError("must supply at least one object to concatenate")
if compat not in _VALID_COMPAT:
raise ValueError(
f"compat={compat!r} invalid: must be 'broadcast_equals', 'equals', 'identical', 'no_conflicts' or 'override'"
)
if isinstance(first_obj, DataArray):
return _dataarray_concat(
objs,
dim=dim,
data_vars=data_vars,
coords=coords,
compat=compat,
positions=positions,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
elif isinstance(first_obj, Dataset):
return _dataset_concat(
objs,
dim=dim,
data_vars=data_vars,
coords=coords,
compat=compat,
positions=positions,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
else:
raise TypeError(
"can only concatenate xarray Dataset and DataArray "
f"objects, got {type(first_obj)}"
)
def _calc_concat_dim_index(
dim_or_data: Hashable | Any,
) -> tuple[Hashable, PandasIndex | None]:
"""Infer the dimension name and 1d index / coordinate variable (if appropriate)
for concatenating along the new dimension.
"""
from xarray.core.dataarray import DataArray
dim: Hashable | None
if isinstance(dim_or_data, str):
dim = dim_or_data
index = None
else:
if not isinstance(dim_or_data, (DataArray, Variable)):
dim = getattr(dim_or_data, "name", None)
if dim is None:
dim = "concat_dim"
else:
(dim,) = dim_or_data.dims
coord_dtype = getattr(dim_or_data, "dtype", None)
index = PandasIndex(dim_or_data, dim, coord_dtype=coord_dtype)
return dim, index
def _calc_concat_over(datasets, dim, dim_names, data_vars: T_DataVars, coords, compat):
"""
Determine which dataset variables need to be concatenated in the result,
"""
# Return values
concat_over = set()
equals = {}
if dim in dim_names:
concat_over_existing_dim = True
concat_over.add(dim)
else:
concat_over_existing_dim = False
concat_dim_lengths = []
for ds in datasets:
if concat_over_existing_dim:
if dim not in ds.dims:
if dim in ds:
ds = ds.set_coords(dim)
concat_over.update(k for k, v in ds.variables.items() if dim in v.dims)
concat_dim_lengths.append(ds.sizes.get(dim, 1))
def process_subset_opt(opt, subset):
if isinstance(opt, str):
if opt == "different":
if compat == "override":
raise ValueError(
f"Cannot specify both {subset}='different' and compat='override'."
)
# all nonindexes that are not the same in each dataset
for k in getattr(datasets[0], subset):
if k not in concat_over:
equals[k] = None
variables = [
ds.variables[k] for ds in datasets if k in ds.variables
]
if len(variables) == 1:
# coords="different" doesn't make sense when only one object
# contains a particular variable.
break
elif len(variables) != len(datasets) and opt == "different":
raise ValueError(
f"{k!r} not present in all datasets and coords='different'. "
f"Either add {k!r} to datasets where it is missing or "
"specify coords='minimal'."
)
# first check without comparing values i.e. no computes
for var in variables[1:]:
equals[k] = getattr(variables[0], compat)(
var, equiv=lazy_array_equiv
)
if equals[k] is not True:
# exit early if we know these are not equal or that
# equality cannot be determined i.e. one or all of
# the variables wraps a numpy array
break
if equals[k] is False:
concat_over.add(k)
elif equals[k] is None:
# Compare the variable of all datasets vs. the one
# of the first dataset. Perform the minimum amount of
# loads in order to avoid multiple loads from disk
# while keeping the RAM footprint low.
v_lhs = datasets[0].variables[k].load()
# We'll need to know later on if variables are equal.
computed = []
for ds_rhs in datasets[1:]:
v_rhs = ds_rhs.variables[k].compute()
computed.append(v_rhs)
if not getattr(v_lhs, compat)(v_rhs):
concat_over.add(k)
equals[k] = False
# computed variables are not to be re-computed
# again in the future
for ds, v in zip(datasets[1:], computed):
ds.variables[k].data = v.data
break
else:
equals[k] = True
elif opt == "all":
concat_over.update(
set().union(
*list(set(getattr(d, subset)) - set(d.dims) for d in datasets)
)
)
elif opt == "minimal":
pass
else:
raise ValueError(f"unexpected value for {subset}: {opt}")
else:
valid_vars = tuple(getattr(datasets[0], subset))
invalid_vars = [k for k in opt if k not in valid_vars]
if invalid_vars:
if subset == "coords":
raise ValueError(
f"the variables {invalid_vars} in coords are not "
f"found in the coordinates of the first dataset {valid_vars}"
)
else:
# note: data_vars are not listed in the error message here,
# because there may be lots of them
raise ValueError(
f"the variables {invalid_vars} in data_vars are not "
f"found in the data variables of the first dataset"
)
concat_over.update(opt)
process_subset_opt(data_vars, "data_vars")
process_subset_opt(coords, "coords")
return concat_over, equals, concat_dim_lengths
# determine dimensional coordinate names and a dict mapping name to DataArray
def _parse_datasets(
datasets: list[T_Dataset],
) -> tuple[
dict[Hashable, Variable],
dict[Hashable, int],
set[Hashable],
set[Hashable],
list[Hashable],
]:
dims: set[Hashable] = set()
all_coord_names: set[Hashable] = set()
data_vars: set[Hashable] = set() # list of data_vars
dim_coords: dict[Hashable, Variable] = {} # maps dim name to variable
dims_sizes: dict[Hashable, int] = {} # shared dimension sizes to expand variables
variables_order: dict[Hashable, Variable] = {} # variables in order of appearance
for ds in datasets:
dims_sizes.update(ds.sizes)
all_coord_names.update(ds.coords)
data_vars.update(ds.data_vars)
variables_order.update(ds.variables)
# preserves ordering of dimensions
for dim in ds.dims:
if dim in dims:
continue
if dim not in dim_coords:
dim_coords[dim] = ds.coords[dim].variable
dims = dims | set(ds.dims)
return dim_coords, dims_sizes, all_coord_names, data_vars, list(variables_order)
def _dataset_concat(
datasets: list[T_Dataset],
dim: str | T_Variable | T_DataArray | pd.Index,
data_vars: T_DataVars,
coords: str | list[str],
compat: CompatOptions,
positions: Iterable[Iterable[int]] | None,
fill_value: Any = dtypes.NA,
join: JoinOptions = "outer",
combine_attrs: CombineAttrsOptions = "override",
) -> T_Dataset:
"""
Concatenate a sequence of datasets along a new or existing dimension
"""
from xarray.core.dataarray import DataArray
from xarray.core.dataset import Dataset
datasets = list(datasets)
if not all(isinstance(dataset, Dataset) for dataset in datasets):
raise TypeError(
"The elements in the input list need to be either all 'Dataset's or all 'DataArray's"
)
if isinstance(dim, DataArray):
dim_var = dim.variable
elif isinstance(dim, Variable):
dim_var = dim
else:
dim_var = None
dim, index = _calc_concat_dim_index(dim)
# Make sure we're working on a copy (we'll be loading variables)
datasets = [ds.copy() for ds in datasets]
datasets = list(
align(*datasets, join=join, copy=False, exclude=[dim], fill_value=fill_value)
)
dim_coords, dims_sizes, coord_names, data_names, vars_order = _parse_datasets(
datasets
)
dim_names = set(dim_coords)
unlabeled_dims = dim_names - coord_names
both_data_and_coords = coord_names & data_names
if both_data_and_coords:
raise ValueError(
f"{both_data_and_coords!r} is a coordinate in some datasets but not others."
)
# we don't want the concat dimension in the result dataset yet
dim_coords.pop(dim, None)
dims_sizes.pop(dim, None)
# case where concat dimension is a coordinate or data_var but not a dimension
if (dim in coord_names or dim in data_names) and dim not in dim_names:
datasets = [ds.expand_dims(dim) for ds in datasets]
# determine which variables to concatenate
concat_over, equals, concat_dim_lengths = _calc_concat_over(
datasets, dim, dim_names, data_vars, coords, compat
)
# determine which variables to merge, and then merge them according to compat
variables_to_merge = (coord_names | data_names) - concat_over - unlabeled_dims
result_vars = {}
result_indexes = {}
if variables_to_merge:
grouped = {
k: v
for k, v in collect_variables_and_indexes(datasets).items()
if k in variables_to_merge
}
merged_vars, merged_indexes = merge_collected(
grouped, compat=compat, equals=equals
)
result_vars.update(merged_vars)
result_indexes.update(merged_indexes)
result_vars.update(dim_coords)
# assign attrs and encoding from first dataset
result_attrs = merge_attrs([ds.attrs for ds in datasets], combine_attrs)
result_encoding = datasets[0].encoding
# check that global attributes are fixed across all datasets if necessary
if compat == "identical":
for ds in datasets[1:]:
if not utils.dict_equiv(ds.attrs, result_attrs):
raise ValueError("Dataset global attributes not equal.")
# we've already verified everything is consistent; now, calculate
# shared dimension sizes so we can expand the necessary variables
def ensure_common_dims(vars, concat_dim_lengths):
# ensure each variable with the given name shares the same
# dimensions and the same shape for all of them except along the
# concat dimension
common_dims = tuple(utils.OrderedSet(d for v in vars for d in v.dims))
if dim not in common_dims:
common_dims = (dim,) + common_dims
for var, dim_len in zip(vars, concat_dim_lengths):
if var.dims != common_dims:
common_shape = tuple(dims_sizes.get(d, dim_len) for d in common_dims)
var = var.set_dims(common_dims, common_shape)
yield var
# get the indexes to concatenate together, create a PandasIndex
# for any scalar coordinate variable found with ``name`` matching ``dim``.
# TODO: depreciate concat a mix of scalar and dimensional indexed coordinates?
# TODO: (benbovy - explicit indexes): check index types and/or coordinates
# of all datasets?
def get_indexes(name):
for ds in datasets:
if name in ds._indexes:
yield ds._indexes[name]
elif name == dim:
var = ds._variables[name]
if not var.dims:
data = var.set_dims(dim).values
yield PandasIndex(data, dim, coord_dtype=var.dtype)
# create concatenation index, needed for later reindexing
file_start_indexes = np.append(0, np.cumsum(concat_dim_lengths))
concat_index = np.arange(file_start_indexes[-1])
concat_index_size = concat_index.size
variable_index_mask = np.ones(concat_index_size, dtype=bool)
# stack up each variable and/or index to fill-out the dataset (in order)
# n.b. this loop preserves variable order, needed for groupby.
ndatasets = len(datasets)
for name in vars_order:
if name in concat_over and name not in result_indexes:
variables = []
# Initialize the mask to all True then set False if any name is missing in
# the datasets:
variable_index_mask.fill(True)
var_concat_dim_length = []
for i, ds in enumerate(datasets):
if name in ds.variables:
variables.append(ds[name].variable)
var_concat_dim_length.append(concat_dim_lengths[i])
else:
# raise if coordinate not in all datasets
if name in coord_names:
raise ValueError(
f"coordinate {name!r} not present in all datasets."
)
# Mask out the indexes without the name:
start = file_start_indexes[i]
end = file_start_indexes[i + 1]
variable_index_mask[slice(start, end)] = False
variable_index = concat_index[variable_index_mask]
vars = ensure_common_dims(variables, var_concat_dim_length)
# Try to concatenate the indexes, concatenate the variables when no index
# is found on all datasets.
indexes: list[Index] = list(get_indexes(name))
if indexes:
if len(indexes) < ndatasets:
raise ValueError(
f"{name!r} must have either an index or no index in all datasets, "
f"found {len(indexes)}/{len(datasets)} datasets with an index."
)
combined_idx = indexes[0].concat(indexes, dim, positions)
if name in datasets[0]._indexes:
idx_vars = datasets[0].xindexes.get_all_coords(name)
else:
# index created from a scalar coordinate
idx_vars = {name: datasets[0][name].variable}
result_indexes.update({k: combined_idx for k in idx_vars})
combined_idx_vars = combined_idx.create_variables(idx_vars)
for k, v in combined_idx_vars.items():
v.attrs = merge_attrs(
[ds.variables[k].attrs for ds in datasets],
combine_attrs=combine_attrs,
)
result_vars[k] = v
else:
combined_var = concat_vars(
vars, dim, positions, combine_attrs=combine_attrs
)
# reindex if variable is not present in all datasets
if len(variable_index) < concat_index_size:
combined_var = reindex_variables(
variables={name: combined_var},
dim_pos_indexers={
dim: pd.Index(variable_index).get_indexer(concat_index)
},
fill_value=fill_value,
)[name]
result_vars[name] = combined_var
elif name in result_vars:
# preserves original variable order
result_vars[name] = result_vars.pop(name)
result = type(datasets[0])(result_vars, attrs=result_attrs)
absent_coord_names = coord_names - set(result.variables)
if absent_coord_names:
raise ValueError(
f"Variables {absent_coord_names!r} are coordinates in some datasets but not others."
)
result = result.set_coords(coord_names)
result.encoding = result_encoding
result = result.drop_vars(unlabeled_dims, errors="ignore")
if index is not None:
# add concat index / coordinate last to ensure that its in the final Dataset
if dim_var is not None:
index_vars = index.create_variables({dim: dim_var})
else:
index_vars = index.create_variables()
result[dim] = index_vars[dim]
result_indexes[dim] = index
# TODO: add indexes at Dataset creation (when it is supported)
result = result._overwrite_indexes(result_indexes)
return result
def _dataarray_concat(
arrays: Iterable[T_DataArray],
dim: str | T_Variable | T_DataArray | pd.Index,
data_vars: T_DataVars,
coords: str | list[str],
compat: CompatOptions,
positions: Iterable[Iterable[int]] | None,
fill_value: object = dtypes.NA,
join: JoinOptions = "outer",
combine_attrs: CombineAttrsOptions = "override",
) -> T_DataArray:
from xarray.core.dataarray import DataArray
arrays = list(arrays)
if not all(isinstance(array, DataArray) for array in arrays):
raise TypeError(
"The elements in the input list need to be either all 'Dataset's or all 'DataArray's"
)
if data_vars != "all":
raise ValueError(
"data_vars is not a valid argument when concatenating DataArray objects"
)
datasets = []
for n, arr in enumerate(arrays):
if n == 0:
name = arr.name
elif name != arr.name:
if compat == "identical":
raise ValueError("array names not identical")
else:
arr = arr.rename(name)
datasets.append(arr._to_temp_dataset())
ds = _dataset_concat(
datasets,
dim,
data_vars,
coords,
compat,
positions,
fill_value=fill_value,
join=join,
combine_attrs=combine_attrs,
)
merged_attrs = merge_attrs([da.attrs for da in arrays], combine_attrs)
result = arrays[0]._from_temp_dataset(ds, name)
result.attrs = merged_attrs
return result
