.. ipython:: python :suppress: import numpy as np import pandas as pd import xarray as xr np.random.seed(123456) np.set_printoptions(threshold=20)
This page gives an overview of the internal design of xarray.
In totality, the Xarray project defines 4 key data structures. In order of increasing complexity, they are:
- :py:class:`xarray.Variable`,
- :py:class:`xarray.DataArray`,
- :py:class:`xarray.Dataset`,
- :py:class:`datatree.DataTree`.
The user guide lists only :py:class:`xarray.DataArray` and :py:class:`xarray.Dataset`, but :py:class:`~xarray.Variable` is the fundamental object internally, and :py:class:`~datatree.DataTree` is a natural generalisation of :py:class:`xarray.Dataset`.
Note
Our :ref:`roadmap` includes plans both to document :py:class:`~xarray.Variable` as fully public API, and to merge the xarray-datatree package into xarray's main repository.
Internally private :ref:`lazy indexing classes <internal design.lazy indexing>` are used to avoid loading more data than necessary, and flexible indexes classes (derived from :py:class:`~xarray.indexes.Index`) provide performant label-based lookups.
The :ref:`data structures` page in the user guide explains the basics and concentrates on user-facing behavior, whereas this section explains how xarray's data structure classes actually work internally.
The core internal data structure in xarray is the :py:class:`~xarray.Variable`, which is used as the basic building block behind xarray's :py:class:`~xarray.Dataset`, :py:class:`~xarray.DataArray` types. A :py:class:`~xarray.Variable` consists of:
dims
: A tuple of dimension names.data
: The N-dimensional array (typically a NumPy or Dask array) storing the Variable's data. It must have the same number of dimensions as the length ofdims
.attrs
: A dictionary of metadata associated with this array. By convention, xarray's built-in operations never use this metadata.encoding
: Another dictionary used to store information about how these variable's data is represented on disk. See :ref:`io.encoding` for more details.
:py:class:`~xarray.Variable` has an interface similar to NumPy arrays, but extended to make use
of named dimensions. For example, it uses dim
in preference to an axis
argument for methods like mean
, and supports :ref:`compute.broadcasting`.
However, unlike Dataset
and DataArray
, the basic Variable
does not
include coordinate labels along each axis.
:py:class:`~xarray.Variable` is public API, but because of its incomplete support for labeled data, it is mostly intended for advanced uses, such as in xarray itself, for writing new backends, or when creating custom indexes. You can access the variable objects that correspond to xarray objects via the (readonly) :py:attr:`Dataset.variables <xarray.Dataset.variables>` and :py:attr:`DataArray.variable <xarray.DataArray.variable>` attributes.
The simplest data structure used by most users is :py:class:`~xarray.DataArray`. A :py:class:`~xarray.DataArray` is a composite object consisting of multiple :py:class:`~xarray.core.variable.Variable` objects which store related data.
A single :py:class:`~xarray.core.Variable` is referred to as the "data variable", and stored under the :py:attr:`~xarray.DataArray.variable`` attribute.
A :py:class:`~xarray.DataArray` inherits all of the properties of this data variable, i.e. dims
, data
, attrs
and encoding
,
all of which are implemented by forwarding on to the underlying Variable
object.
In addition, a :py:class:`~xarray.DataArray` stores additional Variable
objects stored in a dict under the private _coords
attribute,
each of which is referred to as a "Coordinate Variable". These coordinate variable objects are only allowed to have dims
that are a subset of the data variable's dims
,
and each dim has a specific length. This means that the full :py:attr:`~xarray.DataArray.size` of the dataarray can be represented by a dictionary mapping dimension names to integer sizes.
The underlying data variable has this exact same size, and the attached coordinate variables have sizes which are some subset of the size of the data variable.
Another way of saying this is that all coordinate variables must be "alignable" with the data variable.
When a coordinate is accessed by the user (e.g. via the dict-like :py:class:`~xarray.DataArray.__getitem__` syntax),
then a new DataArray
is constructed by finding all coordinate variables that have compatible dimensions and re-attaching them before the result is returned.
This is why most users never see the Variable
class underlying each coordinate variable - it is always promoted to a DataArray
before returning.
Lookups are performed by special :py:class:`~xarray.indexes.Index` objects, which are stored in a dict under the private _indexes
attribute.
Indexes must be associated with one or more coordinates, and essentially act by translating a query given in physical coordinate space
(typically via the :py:meth:`~xarray.DataArray.sel` method) into a set of integer indices in array index space that can be used to index the underlying n-dimensional array-like data
.
Indexing in array index space (typically performed via the :py:meth:`~xarray.DataArray.isel` method) does not require consulting an Index
object.
Finally a :py:class:`~xarray.DataArray` defines a :py:attr:`~xarray.DataArray.name` attribute, which refers to its data
variable but is stored on the wrapping DataArray
class.
The name
attribute is primarily used when one or more :py:class:`~xarray.DataArray` objects are promoted into a :py:class:`~xarray.Dataset`
(e.g. via :py:meth:`~xarray.DataArray.to_dataset`).
Note that the underlying :py:class:`~xarray.core.Variable` objects are all unnamed, so they can always be referred to uniquely via a
dict-like mapping.
The :py:class:`~xarray.Dataset` class is a generalization of the :py:class:`~xarray.DataArray` class that can hold multiple data variables.
Internally all data variables and coordinate variables are stored under a single variables
dict, and coordinates are
specified by storing their names in a private _coord_names
dict.
The dataset's dims
are the set of all dims present across any variable, but (similar to in dataarrays) coordinate
variables cannot have a dimension that is not present on any data variable.
When a data variable or coordinate variable is accessed, a new DataArray
is again constructed from all compatible
coordinates before returning.
Note
The way that selecting a variable from a DataArray
or Dataset
actually involves internally wrapping the
Variable
object back up into a DataArray
/Dataset
is the primary reason :ref:`we recommend against subclassing <internals.accessors.composition>`
Xarray objects. The main problem it creates is that we currently cannot easily guarantee that for example selecting
a coordinate variable from your SubclassedDataArray
would return an instance of SubclassedDataArray
instead
of just an :py:class:`xarray.DataArray`. See GH issue for more details.
If we open a Variable
object from disk using :py:func:`~xarray.open_dataset` we can see that the actual values of
the array wrapped by the data variable are not displayed.
.. ipython:: python da = xr.tutorial.open_dataset("air_temperature")["air"] var = da.variable var
We can see the size, and the dtype of the underlying array, but not the actual values. This is because the values have not yet been loaded.
If we look at the private attribute :py:meth:`~xarray.Variable._data` containing the underlying array object, we see something interesting:
.. ipython:: python var._data
You're looking at one of xarray's internal Lazy Indexing Classes. These powerful classes are hidden from the user, but provide important functionality.
Calling the public :py:attr:`~xarray.Variable.data` property loads the underlying array into memory.
.. ipython:: python var.data
This array is now cached, which we can see by accessing the private attribute again:
.. ipython:: python var._data
The purpose of these lazy indexing classes is to prevent more data being loaded into memory than is necessary for the subsequent analysis, by deferring loading data until after indexing is performed.
Let's open the data from disk again.
.. ipython:: python da = xr.tutorial.open_dataset("air_temperature")["air"] var = da.variable
Now, notice how even after subsetting the data has does not get loaded:
.. ipython:: python var.isel(time=0)
The shape has changed, but the values are still not shown.
Looking at the private attribute again shows how this indexing information was propagated via the hidden lazy indexing classes:
.. ipython:: python var.isel(time=0)._data
Note
Currently only certain indexing operations are lazy, not all array operations. For discussion of making all array operations lazy see GH issue #5081.
Note that xarray's implementation of Lazy Indexing classes is completely separate from how :py:class:`dask.array.Array` objects evaluate lazily. Dask-backed xarray objects delay almost all operations until :py:meth:`~xarray.DataArray.compute` is called (either explicitly or implicitly via :py:meth:`~xarray.DataArray.plot` for example). The exceptions to this laziness are operations whose output shape is data-dependent, such as when calling :py:meth:`~xarray.DataArray.where`.