GroupBy: split-apply-combine

xarray supports “group by” operations with the same API as pandas to implement the split-apply-combine strategy:

  • Split your data into multiple independent groups.
  • Apply some function to each group.
  • Combine your groups back into a single data object.

Group by operations work on both Dataset and DataArray objects. Most of the examples focus on grouping by a single one-dimensional variable, although support for grouping over a multi-dimensional variable has recently been implemented. Note that for one-dimensional data, it is usually faster to rely on pandas’ implementation of the same pipeline.

Split

Let’s create a simple example dataset:

In [1]: ds = xr.Dataset({'foo': (('x', 'y'), np.random.rand(4, 3))},
   ...:                 coords={'x': [10, 20, 30, 40],
   ...:                         'letters': ('x', list('abba'))})
   ...: 

In [2]: arr = ds['foo']

In [3]: ds
Out[3]: 
<xarray.Dataset>
Dimensions:  (x: 4, y: 3)
Coordinates:
    letters  (x) <U1 'a' 'b' 'b' 'a'
  * x        (x) int64 10 20 30 40
Dimensions without coordinates: y
Data variables:
    foo      (x, y) float64 0.127 0.9667 0.2605 0.8972 0.3767 0.3362 0.4514 ...

If we groupby the name of a variable or coordinate in a dataset (we can also use a DataArray directly), we get back a GroupBy object:

In [4]: ds.groupby('letters')
Out[4]: <xarray.core.groupby.DatasetGroupBy at 0x7f534a400cf8>

This object works very similarly to a pandas GroupBy object. You can view the group indices with the groups attribute:

In [5]: ds.groupby('letters').groups
Out[5]: {'a': [0, 3], 'b': [1, 2]}

You can also iterate over groups in (label, group) pairs:

In [6]: list(ds.groupby('letters'))
Out[6]: 
[('a', <xarray.Dataset>
  Dimensions:  (x: 2, y: 3)
  Coordinates:
      letters  (x) <U1 'a' 'a'
    * x        (x) int64 10 40
  Dimensions without coordinates: y
  Data variables:
      foo      (x, y) float64 0.127 0.9667 0.2605 0.543 0.373 0.448),
 ('b', <xarray.Dataset>
  Dimensions:  (x: 2, y: 3)
  Coordinates:
      letters  (x) <U1 'b' 'b'
    * x        (x) int64 20 30
  Dimensions without coordinates: y
  Data variables:
      foo      (x, y) float64 0.8972 0.3767 0.3362 0.4514 0.8403 0.1231)]

Just like in pandas, creating a GroupBy object is cheap: it does not actually split the data until you access particular values.

Binning

Sometimes you don’t want to use all the unique values to determine the groups but instead want to “bin” the data into coarser groups. You could always create a customized coordinate, but xarray facilitates this via the groupby_bins() method.

In [7]: x_bins = [0,25,50]

In [8]: ds.groupby_bins('x', x_bins).groups
Out[8]: 
{Interval(0, 25, closed='right'): [0, 1],
 Interval(25, 50, closed='right'): [2, 3]}

The binning is implemented via pandas.cut, whose documentation details how the bins are assigned. As seen in the example above, by default, the bins are labeled with strings using set notation to precisely identify the bin limits. To override this behavior, you can specify the bin labels explicitly. Here we choose float labels which identify the bin centers:

In [9]: x_bin_labels = [12.5,37.5]

In [10]: ds.groupby_bins('x', x_bins, labels=x_bin_labels).groups
Out[10]: {12.5: [0, 1], 37.5: [2, 3]}

Apply

To apply a function to each group, you can use the flexible apply() method. The resulting objects are automatically concatenated back together along the group axis:

In [11]: def standardize(x):
   ....:     return (x - x.mean()) / x.std()
   ....: 

In [12]: arr.groupby('letters').apply(standardize)
Out[12]: 
<xarray.DataArray 'foo' (x: 4, y: 3)>
array([[-1.229778,  1.93741 , -0.726247],
       [ 1.419796, -0.460192, -0.606579],
       [-0.190642,  1.21398 , -1.376362],
       [ 0.339417, -0.301806, -0.018995]])
Coordinates:
    letters  (x) <U1 'a' 'b' 'b' 'a'
  * x        (x) int64 10 20 30 40
Dimensions without coordinates: y

GroupBy objects also have a reduce() method and methods like mean() as shortcuts for applying an aggregation function:

In [13]: arr.groupby('letters').mean(dim='x')
Out[13]: 
<xarray.DataArray 'foo' (letters: 2, y: 3)>
array([[ 0.334998,  0.669865,  0.354236],
       [ 0.674306,  0.608502,  0.229662]])
Coordinates:
  * letters  (letters) object 'a' 'b'
Dimensions without coordinates: y

Using a groupby is thus also a convenient shortcut for aggregating over all dimensions other than the provided one:

In [14]: ds.groupby('x').std()
Out[14]: 
<xarray.Dataset>
Dimensions:  (x: 4)
Coordinates:
  * x        (x) int64 10 20 30 40
    letters  (x) <U1 'a' 'b' 'b' 'a'
Data variables:
    foo      (x) float64 0.3684 0.2554 0.2931 0.06957

First and last

There are two special aggregation operations that are currently only found on groupby objects: first and last. These provide the first or last example of values for group along the grouped dimension:

In [15]: ds.groupby('letters').first()
Out[15]: 
<xarray.Dataset>
Dimensions:  (letters: 2, y: 3)
Coordinates:
  * letters  (letters) object 'a' 'b'
Dimensions without coordinates: y
Data variables:
    foo      (letters, y) float64 0.127 0.9667 0.2605 0.8972 0.3767 0.3362

By default, they skip missing values (control this with skipna).

Grouped arithmetic

GroupBy objects also support a limited set of binary arithmetic operations, as a shortcut for mapping over all unique labels. Binary arithmetic is supported for (GroupBy, Dataset) and (GroupBy, DataArray) pairs, as long as the dataset or data array uses the unique grouped values as one of its index coordinates. For example:

In [16]: alt = arr.groupby('letters').mean()

In [17]: alt
Out[17]: 
<xarray.DataArray 'foo' (letters: 2)>
array([ 0.453033,  0.504157])
Coordinates:
  * letters  (letters) object 'a' 'b'

In [18]: ds.groupby('letters') - alt
Out[18]: 
<xarray.Dataset>
Dimensions:  (x: 4, y: 3)
Coordinates:
    letters  (x) <U1 'a' 'b' 'b' 'a'
  * x        (x) int64 10 20 30 40
Dimensions without coordinates: y
Data variables:
    foo      (x, y) float64 -0.3261 0.5137 -0.1926 0.3931 -0.1274 -0.1679 ...

This last line is roughly equivalent to the following:

results = []
for label, group in ds.groupby('letters'):
    results.append(group - alt.sel(x=label))
xr.concat(results, dim='x')

Squeezing

When grouping over a dimension, you can control whether the dimension is squeezed out or if it should remain with length one on each group by using the squeeze parameter:

In [19]: next(iter(arr.groupby('x')))
Out[19]: 
(10, <xarray.DataArray 'foo' (y: 3)>
 array([ 0.12697 ,  0.966718,  0.260476])
 Coordinates:
     letters  <U1 'a'
     x        int64 10
 Dimensions without coordinates: y)
In [20]: next(iter(arr.groupby('x', squeeze=False)))
Out[20]: 
(10, <xarray.DataArray 'foo' (x: 1, y: 3)>
 array([[ 0.12697 ,  0.966718,  0.260476]])
 Coordinates:
     letters  (x) <U1 'a'
   * x        (x) int64 10
 Dimensions without coordinates: y)

Although xarray will attempt to automatically transpose dimensions back into their original order when you use apply, it is sometimes useful to set squeeze=False to guarantee that all original dimensions remain unchanged.

You can always squeeze explicitly later with the Dataset or DataArray squeeze() methods.

Multidimensional Grouping

Many datasets have a multidimensional coordinate variable (e.g. longitude) which is different from the logical grid dimensions (e.g. nx, ny). Such variables are valid under the CF conventions. Xarray supports groupby operations over multidimensional coordinate variables:

In [21]: da = xr.DataArray([[0,1],[2,3]],
   ....:     coords={'lon': (['ny','nx'], [[30,40],[40,50]] ),
   ....:             'lat': (['ny','nx'], [[10,10],[20,20]] ),},
   ....:     dims=['ny','nx'])
   ....: 

In [22]: da
Out[22]: 
<xarray.DataArray (ny: 2, nx: 2)>
array([[0, 1],
       [2, 3]])
Coordinates:
    lat      (ny, nx) int64 10 10 20 20
    lon      (ny, nx) int64 30 40 40 50
Dimensions without coordinates: ny, nx

In [23]: da.groupby('lon').sum()
Out[23]: 
<xarray.DataArray (lon: 3)>
array([0, 3, 3])
Coordinates:
  * lon      (lon) int64 30 40 50

In [24]: da.groupby('lon').apply(lambda x: x - x.mean(), shortcut=False)
Out[24]: 
<xarray.DataArray (ny: 2, nx: 2)>
array([[ 0. , -0.5],
       [ 0.5,  0. ]])
Coordinates:
    lat      (ny, nx) int64 10 10 20 20
    lon      (ny, nx) int64 30 40 40 50
Dimensions without coordinates: ny, nx

Because multidimensional groups have the ability to generate a very large number of bins, coarse-binning via groupby_bins() may be desirable:

In [25]: da.groupby_bins('lon', [0,45,50]).sum()
Out[25]: 
<xarray.DataArray (lon_bins: 2)>
array([3, 3])
Coordinates:
  * lon_bins  (lon_bins) object (0, 45] (45, 50]