Working with pandas (original) (raw)

One of the most important features of xarray is the ability to convert to and from pandas objects to interact with the rest of the PyData ecosystem. For example, for plotting labeled data, we highly recommend using the visualization built in to pandas itself or provided by the pandas aware libraries such as Seaborn.

Hierarchical and tidy data#

Tabular data is easiest to work with when it meets the criteria fortidy data:

In this “tidy data” format, we can represent any Dataset andDataArray in terms of DataFrame andSeries, respectively (and vice-versa). The representation works by flattening non-coordinates to 1D, and turning the tensor product of coordinate indexes into a pandas.MultiIndex.

Dataset and DataFrame#

To convert any dataset to a DataFrame in tidy form, use theDataset.to_dataframe() method:

ds = xr.Dataset( {"foo": (("x", "y"), np.random.randn(2, 3))}, coords={ "x": [10, 20], "y": ["a", "b", "c"], "along_x": ("x", np.random.randn(2)), "scalar": 123, }, ) ds

<xarray.Dataset> Size: 100B Dimensions: (x: 2, y: 3) Coordinates:

df = ds.to_dataframe() df

foo along_x scalar
x y
10 a 0.469112 0.119209 123
b -0.282863 0.119209 123
c -1.509059 0.119209 123
20 a -1.135632 -1.044236 123
b 1.212112 -1.044236 123
c -0.173215 -1.044236 123

We see that each variable and coordinate in the Dataset is now a column in the DataFrame, with the exception of indexes which are in the index. To convert the DataFrame to any other convenient representation, use DataFrame methods like reset_index(),stack() and unstack().

For datasets containing dask arrays where the data should be lazily loaded, see theDataset.to_dask_dataframe() method.

To create a Dataset from a DataFrame, use theDataset.from_dataframe() class method or the equivalentpandas.DataFrame.to_xarray() method:

xr.Dataset.from_dataframe(df)

<xarray.Dataset> Size: 184B Dimensions: (x: 2, y: 3) Coordinates:

Notice that the dimensions of variables in the Dataset have now expanded after the round-trip conversion to a DataFrame. This is because every object in a DataFrame must have the same indices, so we need to broadcast the data of each array to the full size of the new MultiIndex.

Likewise, all the coordinates (other than indexes) ended up as variables, because pandas does not distinguish non-index coordinates.

DataArray and Series#

DataArray objects have a complementary representation in terms of aSeries. Using a Series preserves the Dataset toDataArray relationship, because DataFrames are dict-like containers of Series. The methods are very similar to those for working with DataFrames:

s = ds["foo"].to_series() s

x y 10 a 0.469112 b -0.282863 c -1.509059 20 a -1.135632 b 1.212112 c -0.173215 Name: foo, dtype: float64

or equivalently, with Series.to_xarray()

xr.DataArray.from_series(s)

<xarray.DataArray 'foo' (x: 2, y: 3)> Size: 48B array([[ 0.4691123 , -0.28286334, -1.5090585 ], [-1.13563237, 1.21211203, -0.17321465]]) Coordinates:

Both the from_series and from_dataframe methods use reindexing, so they work even if the hierarchical index is not a full tensor product:

x y 10 a 0.469112 c -1.509059 20 b 1.212112 Name: foo, dtype: float64

<xarray.DataArray 'foo' (x: 2, y: 3)> Size: 48B array([[ 0.4691123 , nan, -1.5090585 ], [ nan, 1.21211203, nan]]) Coordinates:

Lossless and reversible conversion#

The previous Dataset example shows that the conversion is not reversible (lossy roundtrip) and that the size of the Dataset increases.

Particularly after a roundtrip, the following deviations are noted:

To avoid these problems, the third-party ntv-pandas library offers lossless and reversible conversions betweenDataset/ DataArray and pandas DataFrame objects.

This solution is particularly interesting for converting any DataFrame into a Dataset (the converter finds the multidimensional structure hidden by the tabular structure).

The ntv-pandas examples show how to improve the conversion for the previous Dataset example and for more complex examples.

Multi-dimensional data#

Tidy data is great, but it sometimes you want to preserve dimensions instead of automatically stacking them into a MultiIndex.

DataArray.to_pandas() is a shortcut that lets you convert a DataArray directly into a pandas object with the same dimensionality, if available in pandas (i.e., a 1D array is converted to aSeries and 2D to DataFrame):

arr = xr.DataArray( np.random.randn(2, 3), coords=[("x", [10, 20]), ("y", ["a", "b", "c"])] ) df = arr.to_pandas() df

y a b c
x
10 -0.861849 -2.104569 -0.494929
20 1.071804 0.721555 -0.706771

To perform the inverse operation of converting any pandas objects into a data array with the same shape, simply use the DataArrayconstructor:

<xarray.DataArray (x: 2, y: 3)> Size: 48B array([[-0.86184896, -2.10456922, -0.49492927], [ 1.07180381, 0.72155516, -0.70677113]]) Coordinates:

Both the DataArray and Dataset constructors directly convert pandas objects into xarray objects with the same shape. This means that they preserve all use of multi-indexes:

index = pd.MultiIndex.from_arrays( [["a", "a", "b"], [0, 1, 2]], names=["one", "two"] ) df = pd.DataFrame({"x": 1, "y": 2}, index=index) ds = xr.Dataset(df) ds

<xarray.Dataset> Size: 120B Dimensions: (dim_0: 3) Coordinates:

However, you will need to set dimension names explicitly, either with thedims argument on in the DataArray constructor or by callingrename on the new object.

Transitioning from pandas.Panel to xarray#

Panel, pandas’ data structure for 3D arrays, was always a second class data structure compared to the Series and DataFrame. To allow pandas developers to focus more on its core functionality built around the DataFrame, pandas removed Panel in favor of directing users who use multi-dimensional arrays to xarray.

Xarray has most of Panel’s features, a more explicit API (particularly around indexing), and the ability to scale to >3 dimensions with the same interface.

As discussed in the data structures section of the docs, there are two primary data structures in xarray: DataArray and Dataset. You can imagine a DataArray as a n-dimensional pandas Series (i.e. a single typed array), and a Datasetas the DataFrame equivalent (i.e. a dict of aligned DataArray objects).

So you can represent a Panel, in two ways:

Let’s take a look:

data = np.random.default_rng(0).random((2, 3, 4)) items = list("ab") major_axis = list("mno") minor_axis = pd.date_range(start="2000", periods=4, name="date")

With old versions of pandas (prior to 0.25), this could stored in a Panel:

pd.Panel(data, items, major_axis, minor_axis)

<class 'pandas.core.panel.Panel'> Dimensions: 2 (items) x 3 (major_axis) x 4 (minor_axis) Items axis: a to b Major_axis axis: m to o Minor_axis axis: 2000-01-01 00:00:00 to 2000-01-04 00:00:00

To put this data in a DataArray, write:

array = xr.DataArray(data, [items, major_axis, minor_axis]) array

<xarray.DataArray (dim_0: 2, dim_1: 3, date: 4)> Size: 192B array([[[0.63696169, 0.26978671, 0.04097352, 0.01652764], [0.81327024, 0.91275558, 0.60663578, 0.72949656], [0.54362499, 0.93507242, 0.81585355, 0.0027385 ]],

   [[0.85740428, 0.03358558, 0.72965545, 0.17565562],
    [0.86317892, 0.54146122, 0.29971189, 0.42268722],
    [0.02831967, 0.12428328, 0.67062441, 0.64718951]]])

Coordinates:

As you can see, there are three dimensions (each is also a coordinate). Two of the axes of were unnamed, so have been assigned dim_0 and dim_1respectively, while the third retains its name date.

You can also easily convert this data into Dataset:

array.to_dataset(dim="dim_0")

<xarray.Dataset> Size: 236B Dimensions: (dim_1: 3, date: 4) Coordinates:

Here, there are two data variables, each representing a DataFrame on panel’sitems axis, and labeled as such. Each variable is a 2D array of the respective values along the items dimension.

While the xarray docs are relatively complete, a few items stand out for Panel users:

While xarray may take some getting used to, it’s worth it! If anything is unclear, please post an issue on GitHub orStackOverflow, and we’ll endeavor to respond to the specific case or improve the general docs.