.. ipython:: python :suppress: import numpy as np import pandas as pd import xarray as xr np.random.seed(123456)
Xarray offers extremely flexible indexing routines that combine the best features of NumPy and pandas for data selection.
The most basic way to access elements of a :py:class:`~xarray.DataArray`
object is to use Python's []
syntax, such as array[i, j]
, where
i
and j
are both integers.
As xarray objects can store coordinates corresponding to each dimension of an
array, label-based indexing similar to pandas.DataFrame.loc
is also possible.
In label-based indexing, the element position i
is automatically
looked-up from the coordinate values.
Dimensions of xarray objects have names, so you can also lookup the dimensions by name, instead of remembering their positional order.
In total, xarray supports four different kinds of indexing, as described below and summarized in this table:
Dimension lookup | Index lookup | DataArray syntax |
Dataset syntax |
---|---|---|---|
Positional | By integer | da[:, 0] |
not available |
Positional | By label | da.loc[:, 'IA'] |
not available |
By name | By integer | da.isel(space=0) or da[dict(space=0)] |
ds.isel(space=0) or ds[dict(space=0)] |
By name | By label | da.sel(space='IA') or da.loc[dict(space='IA')] |
ds.sel(space='IA') or ds.loc[dict(space='IA')] |
More advanced indexing is also possible for all the methods by supplying :py:class:`~xarray.DataArray` objects as indexer. See :ref:`vectorized_indexing` for the details.
Indexing a :py:class:`~xarray.DataArray` directly works (mostly) just like it does for numpy arrays, except that the returned object is always another DataArray:
.. ipython:: python da = xr.DataArray( np.random.rand(4, 3), [ ("time", pd.date_range("2000-01-01", periods=4)), ("space", ["IA", "IL", "IN"]), ], ) da[:2] da[0, 0] da[:, [2, 1]]
Attributes are persisted in all indexing operations.
Warning
Positional indexing deviates from the NumPy when indexing with multiple
arrays like da[[0, 1], [0, 1]]
, as described in
:ref:`vectorized_indexing`.
Xarray also supports label-based indexing, just like pandas. Because we use a :py:class:`pandas.Index` under the hood, label based indexing is very fast. To do label based indexing, use the :py:attr:`~xarray.DataArray.loc` attribute:
.. ipython:: python da.loc["2000-01-01":"2000-01-02", "IA"]
In this example, the selected is a subpart of the array in the range '2000-01-01':'2000-01-02' along the first coordinate time and with 'IA' value from the second coordinate space.
You can perform any of the label indexing operations supported by pandas, including indexing with individual, slices and lists/arrays of labels, as well as indexing with boolean arrays. Like pandas, label based indexing in xarray is inclusive of both the start and stop bounds.
Setting values with label based indexing is also supported:
.. ipython:: python da.loc["2000-01-01", ["IL", "IN"]] = -10 da
With the dimension names, we do not have to rely on dimension order and can use them explicitly to slice data. There are two ways to do this:
Use the :py:meth:`~xarray.DataArray.sel` and :py:meth:`~xarray.DataArray.isel` convenience methods:
.. ipython:: python # index by integer array indices da.isel(space=0, time=slice(None, 2)) # index by dimension coordinate labels da.sel(time=slice("2000-01-01", "2000-01-02"))
Use a dictionary as the argument for array positional or label based array indexing:
.. ipython:: python # index by integer array indices da[dict(space=0, time=slice(None, 2))] # index by dimension coordinate labels da.loc[dict(time=slice("2000-01-01", "2000-01-02"))]
The arguments to these methods can be any objects that could index the array along the dimension given by the keyword, e.g., labels for an individual value, :py:class:`Python slice` objects or 1-dimensional arrays.
Note
We would love to be able to do indexing with labeled dimension names inside
brackets, but unfortunately, Python does not yet support indexing with
keyword arguments like da[space=0]
The label based selection methods :py:meth:`~xarray.Dataset.sel`,
:py:meth:`~xarray.Dataset.reindex` and :py:meth:`~xarray.Dataset.reindex_like` all
support method
and tolerance
keyword argument. The method parameter allows for
enabling nearest neighbor (inexact) lookups by use of the methods 'pad'
,
'backfill'
or 'nearest'
:
.. ipython:: python da = xr.DataArray([1, 2, 3], [("x", [0, 1, 2])]) da.sel(x=[1.1, 1.9], method="nearest") da.sel(x=0.1, method="backfill") da.reindex(x=[0.5, 1, 1.5, 2, 2.5], method="pad")
Tolerance limits the maximum distance for valid matches with an inexact lookup:
.. ipython:: python da.reindex(x=[1.1, 1.5], method="nearest", tolerance=0.2)
The method parameter is not yet supported if any of the arguments
to .sel()
is a slice
object:
.. ipython:: :verbatim: In [1]: da.sel(x=slice(1, 3), method="nearest") NotImplementedError
However, you don't need to use method
to do inexact slicing. Slicing
already returns all values inside the range (inclusive), as long as the index
labels are monotonic increasing:
.. ipython:: python da.sel(x=slice(0.9, 3.1))
Indexing axes with monotonic decreasing labels also works, as long as the
slice
or .loc
arguments are also decreasing:
.. ipython:: python reversed_da = da[::-1] reversed_da.loc[3.1:0.9]
Note
If you want to interpolate along coordinates rather than looking up the nearest neighbors, use :py:meth:`~xarray.Dataset.interp` and :py:meth:`~xarray.Dataset.interp_like`. See :ref:`interpolation <interp>` for the details.
We can also use these methods to index all variables in a dataset simultaneously, returning a new dataset:
.. ipython:: python da = xr.DataArray( np.random.rand(4, 3), [ ("time", pd.date_range("2000-01-01", periods=4)), ("space", ["IA", "IL", "IN"]), ], ) ds = da.to_dataset(name="foo") ds.isel(space=[0], time=[0]) ds.sel(time="2000-01-01")
Positional indexing on a dataset is not supported because the ordering of dimensions in a dataset is somewhat ambiguous (it can vary between different arrays). However, you can do normal indexing with dimension names:
.. ipython:: python ds[dict(space=[0], time=[0])] ds.loc[dict(time="2000-01-01")]
The :py:meth:`~xarray.Dataset.drop_sel` method returns a new object with the listed index labels along a dimension dropped:
.. ipython:: python ds.drop_sel(space=["IN", "IL"])
drop_sel
is both a Dataset
and DataArray
method.
Use :py:meth:`~xarray.Dataset.drop_dims` to drop a full dimension from a Dataset. Any variables with these dimensions are also dropped:
.. ipython:: python ds.drop_dims("time")
Indexing methods on xarray objects generally return a subset of the original data. However, it is sometimes useful to select an object with the same shape as the original data, but with some elements masked. To do this type of selection in xarray, use :py:meth:`~xarray.DataArray.where`:
.. ipython:: python da = xr.DataArray(np.arange(16).reshape(4, 4), dims=["x", "y"]) da.where(da.x + da.y < 4)
This is particularly useful for ragged indexing of multi-dimensional data,
e.g., to apply a 2D mask to an image. Note that where
follows all the
usual xarray broadcasting and alignment rules for binary operations (e.g.,
+
) between the object being indexed and the condition, as described in
:ref:`comput`:
.. ipython:: python da.where(da.y < 2)
By default where
maintains the original size of the data. For cases
where the selected data size is much smaller than the original data,
use of the option drop=True
clips coordinate
elements that are fully masked:
.. ipython:: python da.where(da.y < 2, drop=True)
To check whether elements of an xarray object contain a single object, you can
compare with the equality operator ==
(e.g., arr == 3
). To check
multiple values, use :py:meth:`~xarray.DataArray.isin`:
.. ipython:: python da = xr.DataArray([1, 2, 3, 4, 5], dims=["x"]) da.isin([2, 4])
:py:meth:`~xarray.DataArray.isin` works particularly well with :py:meth:`~xarray.DataArray.where` to support indexing by arrays that are not already labels of an array:
.. ipython:: python lookup = xr.DataArray([-1, -2, -3, -4, -5], dims=["x"]) da.where(lookup.isin([-2, -4]), drop=True)
However, some caution is in order: when done repeatedly, this type of indexing is significantly slower than using :py:meth:`~xarray.DataArray.sel`.
Like numpy and pandas, xarray supports indexing many array elements at once in a vectorized manner.
If you only provide integers, slices, or unlabeled arrays (array without
dimension names, such as np.ndarray
, list
, but not
:py:meth:`~xarray.DataArray` or :py:meth:`~xarray.Variable`) indexing can be
understood as orthogonally. Each indexer component selects independently along
the corresponding dimension, similar to how vector indexing works in Fortran or
MATLAB, or after using the :py:func:`numpy.ix_` helper:
.. ipython:: python da = xr.DataArray( np.arange(12).reshape((3, 4)), dims=["x", "y"], coords={"x": [0, 1, 2], "y": ["a", "b", "c", "d"]}, ) da da[[0, 2, 2], [1, 3]]
For more flexibility, you can supply :py:meth:`~xarray.DataArray` objects as indexers. Dimensions on resultant arrays are given by the ordered union of the indexers' dimensions:
.. ipython:: python ind_x = xr.DataArray([0, 1], dims=["x"]) ind_y = xr.DataArray([0, 1], dims=["y"]) da[ind_x, ind_y] # orthogonal indexing
Slices or sequences/arrays without named-dimensions are treated as if they have the same dimension which is indexed along:
.. ipython:: python # Because [0, 1] is used to index along dimension 'x', # it is assumed to have dimension 'x' da[[0, 1], ind_x]
Furthermore, you can use multi-dimensional :py:meth:`~xarray.DataArray` as indexers, where the resultant array dimension is also determined by indexers' dimension:
.. ipython:: python ind = xr.DataArray([[0, 1], [0, 1]], dims=["a", "b"]) da[ind]
Similar to how NumPy's advanced indexing works, vectorized indexing for xarray is based on our :ref:`broadcasting rules <compute.broadcasting>`. See :ref:`indexing.rules` for the complete specification.
Vectorized indexing also works with isel
, loc
, and sel
:
.. ipython:: python ind = xr.DataArray([[0, 1], [0, 1]], dims=["a", "b"]) da.isel(y=ind) # same as da[:, ind] ind = xr.DataArray([["a", "b"], ["b", "a"]], dims=["a", "b"]) da.loc[:, ind] # same as da.sel(y=ind)
These methods may also be applied to Dataset
objects
.. ipython:: python ds = da.to_dataset(name="bar") ds.isel(x=xr.DataArray([0, 1, 2], dims=["points"]))
Vectorized indexing may be used to extract information from the nearest grid cells of interest, for example, the nearest climate model grid cells to a collection specified weather station latitudes and longitudes. To trigger vectorized indexing behavior you will need to provide the selection dimensions with a new shared output dimension name. In the example below, the selections of the closest latitude and longitude are renamed to an output dimension named "points":
.. ipython:: python ds = xr.tutorial.open_dataset("air_temperature") # Define target latitude and longitude (where weather stations might be) target_lon = xr.DataArray([200, 201, 202, 205], dims="points") target_lat = xr.DataArray([31, 41, 42, 42], dims="points") # Retrieve data at the grid cells nearest to the target latitudes and longitudes da = ds["air"].sel(lon=target_lon, lat=target_lat, method="nearest") da
Tip
If you are lazily loading your data from disk, not every form of vectorized indexing is supported (or if supported, may not be supported efficiently). You may find increased performance by loading your data into memory first, e.g., with :py:meth:`~xarray.Dataset.load`.
Note
If an indexer is a :py:meth:`~xarray.DataArray`, its coordinates should not
conflict with the selected subpart of the target array (except for the
explicitly indexed dimensions with .loc
/.sel
).
Otherwise, IndexError
will be raised.
To select and assign values to a portion of a :py:meth:`~xarray.DataArray` you
can use indexing with .loc
:
.. ipython:: python ds = xr.tutorial.open_dataset("air_temperature") # add an empty 2D dataarray ds["empty"] = xr.full_like(ds.air.mean("time"), fill_value=0) # modify one grid point using loc() ds["empty"].loc[dict(lon=260, lat=30)] = 100 # modify a 2D region using loc() lc = ds.coords["lon"] la = ds.coords["lat"] ds["empty"].loc[ dict(lon=lc[(lc > 220) & (lc < 260)], lat=la[(la > 20) & (la < 60)]) ] = 100
.. ipython:: python # modify one grid point using xr.where() ds["empty"] = xr.where( (ds.coords["lat"] == 20) & (ds.coords["lon"] == 260), 100, ds["empty"] ) # or modify a 2D region using xr.where() mask = ( (ds.coords["lat"] > 20) & (ds.coords["lat"] < 60) & (ds.coords["lon"] > 220) & (ds.coords["lon"] < 260) ) ds["empty"] = xr.where(mask, 100, ds["empty"])
Vectorized indexing can also be used to assign values to xarray object.
.. ipython:: python da = xr.DataArray( np.arange(12).reshape((3, 4)), dims=["x", "y"], coords={"x": [0, 1, 2], "y": ["a", "b", "c", "d"]}, ) da da[0] = -1 # assignment with broadcasting da ind_x = xr.DataArray([0, 1], dims=["x"]) ind_y = xr.DataArray([0, 1], dims=["y"]) da[ind_x, ind_y] = -2 # assign -2 to (ix, iy) = (0, 0) and (1, 1) da da[ind_x, ind_y] += 100 # increment is also possible da
Like numpy.ndarray
, value assignment sometimes works differently from what one may expect.
.. ipython:: python da = xr.DataArray([0, 1, 2, 3], dims=["x"]) ind = xr.DataArray([0, 0, 0], dims=["x"]) da[ind] -= 1 da
Where the 0th element will be subtracted 1 only once.
This is because v[0] = v[0] - 1
is called three times, rather than
v[0] = v[0] - 1 - 1 - 1
.
See Assigning values to indexed arrays for the details.
Note
Dask array does not support value assignment (see :ref:`dask` for the details).
Note
Coordinates in both the left- and right-hand-side arrays should not
conflict with each other.
Otherwise, IndexError
will be raised.
Warning
Do not try to assign values when using any of the indexing methods isel
or sel
:
# DO NOT do this da.isel(space=0) = 0
Instead, values can be assigned using dictionary-based indexing:
da[dict(space=0)] = 0
Assigning values with the chained indexing using .sel
or .isel
fails silently.
.. ipython:: python da = xr.DataArray([0, 1, 2, 3], dims=["x"]) # DO NOT do this da.isel(x=[0, 1, 2])[1] = -1 da
You can also assign values to all variables of a :py:class:`Dataset` at once:
.. ipython:: python ds_org = xr.tutorial.open_dataset("eraint_uvz").isel( latitude=slice(56, 59), longitude=slice(255, 258), level=0 ) # set all values to 0 ds = xr.zeros_like(ds_org) ds # by integer ds[dict(latitude=2, longitude=2)] = 1 ds["u"] ds["v"] # by label ds.loc[dict(latitude=47.25, longitude=[11.25, 12])] = 100 ds["u"] # dataset as new values new_dat = ds_org.loc[dict(latitude=48, longitude=[11.25, 12])] new_dat ds.loc[dict(latitude=47.25, longitude=[11.25, 12])] = new_dat ds["u"]
The dimensions can differ between the variables in the dataset, but all variables need to have at least the dimensions specified in the indexer dictionary. The new values must be either a scalar, a :py:class:`DataArray` or a :py:class:`Dataset` itself that contains all variables that also appear in the dataset to be modified.
The use of :py:meth:`~xarray.DataArray` objects as indexers enables very flexible indexing. The following is an example of the pointwise indexing:
.. ipython:: python da = xr.DataArray(np.arange(56).reshape((7, 8)), dims=["x", "y"]) da da.isel(x=xr.DataArray([0, 1, 6], dims="z"), y=xr.DataArray([0, 1, 0], dims="z"))
where three elements at (ix, iy) = ((0, 0), (1, 1), (6, 0))
are selected
and mapped along a new dimension z
.
If you want to add a coordinate to the new dimension z
,
you can supply a :py:class:`~xarray.DataArray` with a coordinate,
.. ipython:: python da.isel( x=xr.DataArray([0, 1, 6], dims="z", coords={"z": ["a", "b", "c"]}), y=xr.DataArray([0, 1, 0], dims="z"), )
Analogously, label-based pointwise-indexing is also possible by the .sel
method:
.. ipython:: python da = xr.DataArray( np.random.rand(4, 3), [ ("time", pd.date_range("2000-01-01", periods=4)), ("space", ["IA", "IL", "IN"]), ], ) times = xr.DataArray( pd.to_datetime(["2000-01-03", "2000-01-02", "2000-01-01"]), dims="new_time" ) da.sel(space=xr.DataArray(["IA", "IL", "IN"], dims=["new_time"]), time=times)
Xarray's reindex
, reindex_like
and align
impose a DataArray
or
Dataset
onto a new set of coordinates corresponding to dimensions. The
original values are subset to the index labels still found in the new labels,
and values corresponding to new labels not found in the original object are
in-filled with NaN.
Xarray operations that combine multiple objects generally automatically align their arguments to share the same indexes. However, manual alignment can be useful for greater control and for increased performance.
To reindex a particular dimension, use :py:meth:`~xarray.DataArray.reindex`:
.. ipython:: python da.reindex(space=["IA", "CA"])
The :py:meth:`~xarray.DataArray.reindex_like` method is a useful shortcut. To demonstrate, we will make a subset DataArray with new values:
.. ipython:: python foo = da.rename("foo") baz = (10 * da[:2, :2]).rename("baz") baz
Reindexing foo
with baz
selects out the first two values along each
dimension:
.. ipython:: python foo.reindex_like(baz)
The opposite operation asks us to reindex to a larger shape, so we fill in the missing values with NaN:
.. ipython:: python baz.reindex_like(foo)
The :py:func:`~xarray.align` function lets us perform more flexible database-like
'inner'
, 'outer'
, 'left'
and 'right'
joins:
.. ipython:: python xr.align(foo, baz, join="inner") xr.align(foo, baz, join="outer")
Both reindex_like
and align
work interchangeably between
:py:class:`~xarray.DataArray` and :py:class:`~xarray.Dataset` objects, and with any number of matching dimension names:
.. ipython:: python ds ds.reindex_like(baz) other = xr.DataArray(["a", "b", "c"], dims="other") # this is a no-op, because there are no shared dimension names ds.reindex_like(other)
Coordinate labels for each dimension are optional (as of xarray v0.9). Label
based indexing with .sel
and .loc
uses standard positional,
integer-based indexing as a fallback for dimensions without a coordinate label:
.. ipython:: python da = xr.DataArray([1, 2, 3], dims="x") da.sel(x=[0, -1])
Alignment between xarray objects where one or both do not have coordinate labels succeeds only if all dimensions of the same name have the same length. Otherwise, it raises an informative error:
.. ipython:: :verbatim: In [62]: xr.align(da, da[:2]) ValueError: arguments without labels along dimension 'x' cannot be aligned because they have different dimension sizes: {2, 3}
Xarray uses the :py:class:`pandas.Index` internally to perform indexing operations. If you need to access the underlying indexes, they are available through the :py:attr:`~xarray.DataArray.indexes` attribute.
.. ipython:: python da = xr.DataArray( np.random.rand(4, 3), [ ("time", pd.date_range("2000-01-01", periods=4)), ("space", ["IA", "IL", "IN"]), ], ) da da.indexes da.indexes["time"]
Use :py:meth:`~xarray.DataArray.get_index` to get an index for a dimension, falling back to a default :py:class:`pandas.RangeIndex` if it has no coordinate labels:
.. ipython:: python da = xr.DataArray([1, 2, 3], dims="x") da da.get_index("x")
Whether array indexing returns a view or a copy of the underlying data depends on the nature of the labels.
For positional (integer) indexing, xarray follows the same rules as NumPy:
- Positional indexing with only integers and slices returns a view.
- Positional indexing with arrays or lists returns a copy.
The rules for label based indexing are more complex:
- Label-based indexing with only slices returns a view.
- Label-based indexing with arrays returns a copy.
- Label-based indexing with scalars returns a view or a copy, depending upon if the corresponding positional indexer can be represented as an integer or a slice object. The exact rules are determined by pandas.
Whether data is a copy or a view is more predictable in xarray than in pandas, so unlike pandas, xarray does not produce SettingWithCopy warnings. However, you should still avoid assignment with chained indexing.
Just like pandas, advanced indexing on multi-level indexes is possible with
loc
and sel
. You can slice a multi-index by providing multiple indexers,
i.e., a tuple of slices, labels, list of labels, or any selector allowed by
pandas:
.. ipython:: python midx = pd.MultiIndex.from_product([list("abc"), [0, 1]], names=("one", "two")) mda = xr.DataArray(np.random.rand(6, 3), [("x", midx), ("y", range(3))]) mda mda.sel(x=(list("ab"), [0]))
You can also select multiple elements by providing a list of labels or tuples or a slice of tuples:
.. ipython:: python mda.sel(x=[("a", 0), ("b", 1)])
Additionally, xarray supports dictionaries:
.. ipython:: python mda.sel(x={"one": "a", "two": 0})
For convenience, sel
also accepts multi-index levels directly
as keyword arguments:
.. ipython:: python mda.sel(one="a", two=0)
Note that using sel
it is not possible to mix a dimension
indexer with level indexers for that dimension
(e.g., mda.sel(x={'one': 'a'}, two=0)
will raise a ValueError
).
Like pandas, xarray handles partial selection on multi-index (level drop). As shown below, it also renames the dimension / coordinate when the multi-index is reduced to a single index.
.. ipython:: python mda.loc[{"one": "a"}, ...]
Unlike pandas, xarray does not guess whether you provide index levels or
dimensions when using loc
in some ambiguous cases. For example, for
mda.loc[{'one': 'a', 'two': 0}]
and mda.loc['a', 0]
xarray
always interprets ('one', 'two') and ('a', 0) as the names and
labels of the 1st and 2nd dimension, respectively. You must specify all
dimensions or use the ellipsis in the loc
specifier, e.g. in the example
above, mda.loc[{'one': 'a', 'two': 0}, :]
or mda.loc[('a', 0), ...]
.
Here we describe the full rules xarray uses for vectorized indexing. Note that this is for the purposes of explanation: for the sake of efficiency and to support various backends, the actual implementation is different.
- (Only for label based indexing.) Look up positional indexes along each dimension from the corresponding :py:class:`pandas.Index`.
- A full slice object
:
is inserted for each dimension without an indexer. slice
objects are converted into arrays, given bynp.arange(*slice.indices(...))
.- Assume dimension names for array indexers without dimensions, such as
np.ndarray
andlist
, from the dimensions to be indexed along. For example,v.isel(x=[0, 1])
is understood asv.isel(x=xr.DataArray([0, 1], dims=['x']))
. - For each variable in a
Dataset
orDataArray
(the array and its coordinates):- Broadcast all relevant indexers based on their dimension names (see :ref:`compute.broadcasting` for full details).
- Index the underling array by the broadcast indexers, using NumPy's advanced indexing rules.
- If any indexer DataArray has coordinates and no coordinate with the same name exists, attach them to the indexed object.
Note
Only 1-dimensional boolean arrays can be used as indexers.