data-structures.rst

Data Structures

.. ipython:: python
   :suppress:

    import numpy as np
    import pandas as pd
    import xarray as xr
    np.random.seed(123456)
    np.set_printoptions(threshold=10)

DataArray

:py:class:`xarray.DataArray` is xarray's implementation of a labeled, multi-dimensional array. It has several key properties:

• values: a :py:class:`numpy.ndarray` holding the array's values
• dims: dimension names for each axis (e.g., ('x', 'y', 'z'))
• coords: a dict-like container of arrays (coordinates) that label each point (e.g., 1-dimensional arrays of numbers, datetime objects or strings)
• attrs: an OrderedDict to hold arbitrary metadata (attributes)

xarray uses dims and coords to enable its core metadata aware operations. Dimensions provide names that xarray uses instead of the axis argument found in many numpy functions. Coordinates enable fast label based indexing and alignment, building on the functionality of the index found on a pandas :py:class:`~pandas.DataFrame` or :py:class:`~pandas.Series`.

DataArray objects also can have a name and can hold arbitrary metadata in the form of their attrs property (an ordered dictionary). Names and attributes are strictly for users and user-written code: xarray makes no attempt to interpret them, and propagates them only in unambiguous cases (see FAQ, :ref:`approach to metadata`).

Creating a DataArray

The :py:class:`~xarray.DataArray` constructor takes:

• data: a multi-dimensional array of values (e.g., a numpy ndarray, :py:class:`~pandas.Series`, :py:class:`~pandas.DataFrame` or :py:class:`~pandas.Panel`)
• coords: a list or dictionary of coordinates. If a list, it should be a list of tuples where the first element is the dimension name and the second element is the corresponding coordinate array_like object.
• dims: a list of dimension names. If omitted and coords is a list of tuples, dimension names are taken from coords.
• attrs: a dictionary of attributes to add to the instance
• name: a string that names the instance

.. ipython:: python

    data = np.random.rand(4, 3)
    locs = ['IA', 'IL', 'IN']
    times = pd.date_range('2000-01-01', periods=4)
    foo = xr.DataArray(data, coords=[times, locs], dims=['time', 'space'])
    foo

Only data is required; all of other arguments will be filled in with default values:

.. ipython:: python

    xr.DataArray(data)

As you can see, dimension names are always present in the xarray data model: if you do not provide them, defaults of the form dim_N will be created. However, coordinates are always optional, and dimensions do not have automatic coordinate labels.

Note

This is different from pandas, where axes always have tick labels, which default to the integers [0, ..., n-1].

Prior to xarray v0.9, xarray copied this behavior: default coordinates for each dimension would be created if coordinates were not supplied explicitly. This is no longer the case.

Coordinates can be specified in the following ways:

• A list of values with length equal to the number of dimensions, providing coordinate labels for each dimension. Each value must be of one of the following forms:
  • A :py:class:`~xarray.DataArray` or :py:class:`~xarray.Variable`
  • A tuple of the form (dims, data[, attrs]), which is converted into arguments for :py:class:`~xarray.Variable`
  • A pandas object or scalar value, which is converted into a DataArray
  • A 1D array or list, which is interpreted as values for a one dimensional coordinate variable along the same dimension as it's name
• A dictionary of {coord_name: coord} where values are of the same form as the list. Supplying coordinates as a dictionary allows other coordinates than those corresponding to dimensions (more on these later). If you supply coords as a dictionary, you must explicitly provide dims.

As a list of tuples:

.. ipython:: python

    xr.DataArray(data, coords=[('time', times), ('space', locs)])

As a dictionary:

.. ipython:: python

    xr.DataArray(data, coords={'time': times, 'space': locs, 'const': 42,
                               'ranking': ('space', [1, 2, 3])},
                 dims=['time', 'space'])

As a dictionary with coords across multiple dimensions:

.. ipython:: python

    xr.DataArray(data, coords={'time': times, 'space': locs, 'const': 42,
                               'ranking': (('time', 'space'), np.arange(12).reshape(4,3))},
                 dims=['time', 'space'])

If you create a DataArray by supplying a pandas :py:class:`~pandas.Series`, :py:class:`~pandas.DataFrame` or :py:class:`~pandas.Panel`, any non-specified arguments in the DataArray constructor will be filled in from the pandas object:

.. ipython:: python

    df = pd.DataFrame({'x': [0, 1], 'y': [2, 3]}, index=['a', 'b'])
    df.index.name = 'abc'
    df.columns.name = 'xyz'
    df
    xr.DataArray(df)

DataArray properties

Let's take a look at the important properties on our array:

.. ipython:: python

    foo.values
    foo.dims
    foo.coords
    foo.attrs
    print(foo.name)

You can modify values inplace:

.. ipython:: python

   foo.values = 1.0 * foo.values

Note

The array values in a :py:class:`~xarray.DataArray` have a single (homogeneous) data type. To work with heterogeneous or structured data types in xarray, use coordinates, or put separate DataArray objects in a single :py:class:`~xarray.Dataset` (see below).

Now fill in some of that missing metadata:

.. ipython:: python

    foo.name = 'foo'
    foo.attrs['units'] = 'meters'
    foo

The :py:meth:`~xarray.DataArray.rename` method is another option, returning a new data array:

.. ipython:: python

   foo.rename('bar')

DataArray Coordinates

The coords property is dict like. Individual coordinates can be accessed from the coordinates by name, or even by indexing the data array itself:

.. ipython:: python

    foo.coords['time']
    foo['time']

These are also :py:class:`~xarray.DataArray` objects, which contain tick-labels for each dimension.

Coordinates can also be set or removed by using the dictionary like syntax:

.. ipython:: python

    foo['ranking'] = ('space', [1, 2, 3])
    foo.coords
    del foo['ranking']
    foo.coords

For more details, see :ref:`coordinates` below.

Dataset

:py:class:`xarray.Dataset` is xarray's multi-dimensional equivalent of a :py:class:`~pandas.DataFrame`. It is a dict-like container of labeled arrays (:py:class:`~xarray.DataArray` objects) with aligned dimensions. It is designed as an in-memory representation of the data model from the netCDF file format.

In addition to the dict-like interface of the dataset itself, which can be used to access any variable in a dataset, datasets have four key properties:

• dims: a dictionary mapping from dimension names to the fixed length of each dimension (e.g., {'x': 6, 'y': 6, 'time': 8})
• data_vars: a dict-like container of DataArrays corresponding to variables
• coords: another dict-like container of DataArrays intended to label points used in data_vars (e.g., arrays of numbers, datetime objects or strings)
• attrs: an OrderedDict to hold arbitrary metadata

The distinction between whether a variables falls in data or coordinates (borrowed from CF conventions) is mostly semantic, and you can probably get away with ignoring it if you like: dictionary like access on a dataset will supply variables found in either category. However, xarray does make use of the distinction for indexing and computations. Coordinates indicate constant/fixed/independent quantities, unlike the varying/measured/dependent quantities that belong in data.

Here is an example of how we might structure a dataset for a weather forecast:

In this example, it would be natural to call temperature and precipitation "data variables" and all the other arrays "coordinate variables" because they label the points along the dimensions. (see [1] for more background on this example).

Creating a Dataset

To make an :py:class:`~xarray.Dataset` from scratch, supply dictionaries for any variables (data_vars), coordinates (coords) and attributes (attrs).

• data_vars should be a dictionary with each key as the name of the variable and each value as one of:
  • A :py:class:`~xarray.DataArray` or :py:class:`~xarray.Variable`
  • A tuple of the form (dims, data[, attrs]), which is converted into arguments for :py:class:`~xarray.Variable`
  • A pandas object, which is converted into a DataArray
  • A 1D array or list, which is interpreted as values for a one dimensional coordinate variable along the same dimension as it's name
• coords should be a dictionary of the same form as data_vars.
• attrs should be a dictionary.

Let's create some fake data for the example we show above:

.. ipython:: python

    temp = 15 + 8 * np.random.randn(2, 2, 3)
    precip = 10 * np.random.rand(2, 2, 3)
    lon = [[-99.83, -99.32], [-99.79, -99.23]]
    lat = [[42.25, 42.21], [42.63, 42.59]]

    # for real use cases, its good practice to supply array attributes such as
    # units, but we won't bother here for the sake of brevity
    ds = xr.Dataset({'temperature': (['x', 'y', 'time'],  temp),
                     'precipitation': (['x', 'y', 'time'], precip)},
                    coords={'lon': (['x', 'y'], lon),
                            'lat': (['x', 'y'], lat),
                            'time': pd.date_range('2014-09-06', periods=3),
                            'reference_time': pd.Timestamp('2014-09-05')})
    ds

Here we pass :py:class:`xarray.DataArray` objects or a pandas object as values in the dictionary:

.. ipython:: python

    xr.Dataset({'bar': foo})

.. ipython:: python

    xr.Dataset({'bar': foo.to_pandas()})

Where a pandas object is supplied as a value, the names of its indexes are used as dimension names, and its data is aligned to any existing dimensions.

You can also create an dataset from:

• A :py:class:`pandas.DataFrame` or :py:class:`pandas.Panel` along its columns and items respectively, by passing it into the :py:class:`~xarray.Dataset` directly
• A :py:class:`pandas.DataFrame` with :py:meth:`Dataset.from_dataframe <xarray.Dataset.from_dataframe>`, which will additionally handle MultiIndexes See :ref:`pandas`
• A netCDF file on disk with :py:func:`~xarray.open_dataset`. See :ref:`io`.

Dataset contents

:py:class:`~xarray.Dataset` implements the Python mapping interface, with values given by :py:class:`xarray.DataArray` objects:

.. ipython:: python

    'temperature' in ds
    ds['temperature']

Valid keys include each listed coordinate and data variable.

Data and coordinate variables are also contained separately in the :py:attr:`~xarray.Dataset.data_vars` and :py:attr:`~xarray.Dataset.coords` dictionary-like attributes:

.. ipython:: python

    ds.data_vars
    ds.coords

Finally, like data arrays, datasets also store arbitrary metadata in the form of attributes:

.. ipython:: python

    ds.attrs

    ds.attrs['title'] = 'example attribute'
    ds

xarray does not enforce any restrictions on attributes, but serialization to some file formats may fail if you use objects that are not strings, numbers or :py:class:`numpy.ndarray` objects.

As a useful shortcut, you can use attribute style access for reading (but not setting) variables and attributes:

.. ipython:: python

    ds.temperature

This is particularly useful in an exploratory context, because you can tab-complete these variable names with tools like IPython.

Dictionary like methods

We can update a dataset in-place using Python's standard dictionary syntax. For example, to create this example dataset from scratch, we could have written:

.. ipython:: python

    ds = xr.Dataset()
    ds['temperature'] = (('x', 'y', 'time'), temp)
    ds['temperature_double'] = (('x', 'y', 'time'), temp * 2 )
    ds['precipitation'] = (('x', 'y', 'time'), precip)
    ds.coords['lat'] = (('x', 'y'), lat)
    ds.coords['lon'] = (('x', 'y'), lon)
    ds.coords['time'] = pd.date_range('2014-09-06', periods=3)
    ds.coords['reference_time'] = pd.Timestamp('2014-09-05')

To change the variables in a Dataset, you can use all the standard dictionary methods, including values, items, __delitem__, get and :py:meth:`~xarray.Dataset.update`. Note that assigning a DataArray or pandas object to a Dataset variable using __setitem__ or update will :ref:`automatically align<update>` the array(s) to the original dataset's indexes.

You can copy a Dataset by calling the :py:meth:`~xarray.Dataset.copy` method. By default, the copy is shallow, so only the container will be copied: the arrays in the Dataset will still be stored in the same underlying :py:class:`numpy.ndarray` objects. You can copy all data by calling ds.copy(deep=True).

Transforming datasets

In addition to dictionary-like methods (described above), xarray has additional methods (like pandas) for transforming datasets into new objects.

For removing variables, you can select and drop an explicit list of variables by indexing with a list of names or using the :py:meth:`~xarray.Dataset.drop` methods to return a new Dataset. These operations keep around coordinates:

.. ipython:: python

    ds[['temperature']]
    ds[['temperature', 'temperature_double']]
    ds.drop('temperature')

To remove a dimension, you can use :py:meth:`~xarray.Dataset.drop_dims` method. Any variables using that dimension are dropped:

.. ipython:: python

    ds.drop_dims('time')

As an alternate to dictionary-like modifications, you can use :py:meth:`~xarray.Dataset.assign` and :py:meth:`~xarray.Dataset.assign_coords`. These methods return a new dataset with additional (or replaced) or values:

.. ipython:: python

    ds.assign(temperature2 = 2 * ds.temperature)

There is also the :py:meth:`~xarray.Dataset.pipe` method that allows you to use a method call with an external function (e.g., ds.pipe(func)) instead of simply calling it (e.g., func(ds)). This allows you to write pipelines for transforming you data (using "method chaining") instead of writing hard to follow nested function calls:

.. ipython:: python

    # these lines are equivalent, but with pipe we can make the logic flow
    # entirely from left to right
    plt.plot((2 * ds.temperature.sel(x=0)).mean('y'))
    (ds.temperature
     .sel(x=0)
     .pipe(lambda x: 2 * x)
     .mean('y')
     .pipe(plt.plot))

Both pipe and assign replicate the pandas methods of the same names (:py:meth:`DataFrame.pipe <pandas.DataFrame.pipe>` and :py:meth:`DataFrame.assign <pandas.DataFrame.assign>`).

With xarray, there is no performance penalty for creating new datasets, even if variables are lazily loaded from a file on disk. Creating new objects instead of mutating existing objects often results in easier to understand code, so we encourage using this approach.

Renaming variables

Another useful option is the :py:meth:`~xarray.Dataset.rename` method to rename dataset variables:

.. ipython:: python

    ds.rename({'temperature': 'temp', 'precipitation': 'precip'})

The related :py:meth:`~xarray.Dataset.swap_dims` method allows you do to swap dimension and non-dimension variables:

.. ipython:: python

    ds.coords['day'] = ('time', [6, 7, 8])
    ds.swap_dims({'time': 'day'})

Coordinates

Coordinates are ancillary variables stored for DataArray and Dataset objects in the coords attribute:

.. ipython:: python

    ds.coords

Unlike attributes, xarray does interpret and persist coordinates in operations that transform xarray objects. There are two types of coordinates in xarray:

• dimension coordinates are one dimensional coordinates with a name equal to their sole dimension (marked by * when printing a dataset or data array). They are used for label based indexing and alignment, like the index found on a pandas :py:class:`~pandas.DataFrame` or :py:class:`~pandas.Series`. Indeed, these "dimension" coordinates use a :py:class:`pandas.Index` internally to store their values.
• non-dimension coordinates are variables that contain coordinate data, but are not a dimension coordinate. They can be multidimensional (see :ref:`examples.multidim`), and there is no relationship between the name of a non-dimension coordinate and the name(s) of its dimension(s). Non-dimension coordinates can be useful for indexing or plotting; otherwise, xarray does not make any direct use of the values associated with them. They are not used for alignment or automatic indexing, nor are they required to match when doing arithmetic (see :ref:`coordinates math`).

Note

xarray's terminology differs from the CF terminology, where the "dimension coordinates" are called "coordinate variables", and the "non-dimension coordinates" are called "auxiliary coordinate variables" (see :issue:`1295` for more details).

Modifying coordinates

To entirely add or remove coordinate arrays, you can use dictionary like syntax, as shown above.

To convert back and forth between data and coordinates, you can use the :py:meth:`~xarray.Dataset.set_coords` and :py:meth:`~xarray.Dataset.reset_coords` methods:

.. ipython:: python

    ds.reset_coords()
    ds.set_coords(['temperature', 'precipitation'])
    ds['temperature'].reset_coords(drop=True)

Notice that these operations skip coordinates with names given by dimensions, as used for indexing. This mostly because we are not entirely sure how to design the interface around the fact that xarray cannot store a coordinate and variable with the name but different values in the same dictionary. But we do recognize that supporting something like this would be useful.

Coordinates methods

Coordinates objects also have a few useful methods, mostly for converting them into dataset objects:

.. ipython:: python

    ds.coords.to_dataset()

The merge method is particularly interesting, because it implements the same logic used for merging coordinates in arithmetic operations (see :ref:`comput`):

.. ipython:: python

    alt = xr.Dataset(coords={'z': [10], 'lat': 0, 'lon': 0})
    ds.coords.merge(alt.coords)

The coords.merge method may be useful if you want to implement your own binary operations that act on xarray objects. In the future, we hope to write more helper functions so that you can easily make your functions act like xarray's built-in arithmetic.

Indexes

To convert a coordinate (or any DataArray) into an actual :py:class:`pandas.Index`, use the :py:meth:`~xarray.DataArray.to_index` method:

.. ipython:: python

    ds['time'].to_index()

A useful shortcut is the indexes property (on both DataArray and Dataset), which lazily constructs a dictionary whose keys are given by each dimension and whose the values are Index objects:

.. ipython:: python

    ds.indexes

MultiIndex coordinates

Xarray supports labeling coordinate values with a :py:class:`pandas.MultiIndex`:

.. ipython:: python

    midx = pd.MultiIndex.from_arrays([['R', 'R', 'V', 'V'], [.1, .2, .7, .9]],
                                     names=('band', 'wn'))
    mda = xr.DataArray(np.random.rand(4), coords={'spec': midx}, dims='spec')
    mda

For convenience multi-index levels are directly accessible as "virtual" or "derived" coordinates (marked by - when printing a dataset or data array):

.. ipython:: python

     mda['band']
     mda.wn

Indexing with multi-index levels is also possible using the sel method (see :ref:`multi-level indexing`).

Unlike other coordinates, "virtual" level coordinates are not stored in the coords attribute of DataArray and Dataset objects (although they are shown when printing the coords attribute). Consequently, most of the coordinates related methods don't apply for them. It also can't be used to replace one particular level.

Because in a DataArray or Dataset object each multi-index level is accessible as a "virtual" coordinate, its name must not conflict with the names of the other levels, coordinates and data variables of the same object. Even though Xarray set default names for multi-indexes with unnamed levels, it is recommended that you explicitly set the names of the levels.

[1]	Latitude and longitude are 2D arrays because the dataset uses projected coordinates. reference_time refers to the reference time at which the forecast was made, rather than time which is the valid time for which the forecast applies.